Query 030808
Match_columns 171
No_of_seqs 125 out of 185
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 04:53:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030808.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030808hhsearch_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 1.8E-20 4E-25 125.5 4.5 54 45-98 1-54 (54)
2 PF14571 Di19_C: Stress-induce 99.2 9.5E-12 2.1E-16 94.6 1.3 37 119-155 1-45 (105)
3 KOG1280 Uncharacterized conser 98.8 5.6E-09 1.2E-13 94.2 3.8 72 25-98 59-141 (381)
4 PF13894 zf-C2H2_4: C2H2-type 94.7 0.025 5.3E-07 30.3 1.8 23 47-69 1-24 (24)
5 KOG2923 Uncharacterized conser 94.6 0.016 3.5E-07 41.7 1.1 45 32-85 7-54 (67)
6 COG5216 Uncharacterized conser 94.1 0.021 4.6E-07 40.8 0.9 45 32-85 7-54 (67)
7 PF13913 zf-C2HC_2: zinc-finge 93.5 0.068 1.5E-06 31.1 2.2 21 46-66 2-22 (25)
8 PF09237 GAGA: GAGA factor; I 92.8 0.056 1.2E-06 37.5 1.3 27 73-99 22-50 (54)
9 PF00096 zf-C2H2: Zinc finger, 92.5 0.079 1.7E-06 28.9 1.4 21 47-67 1-22 (23)
10 PLN03086 PRLI-interacting fact 92.4 0.16 3.4E-06 49.0 4.1 48 44-96 451-499 (567)
11 COG5236 Uncharacterized conser 91.8 0.12 2.7E-06 48.0 2.6 89 45-142 219-349 (493)
12 PF12756 zf-C2H2_2: C2H2 type 90.2 0.16 3.6E-06 35.2 1.4 48 49-96 2-73 (100)
13 smart00531 TFIIE Transcription 89.5 0.29 6.3E-06 38.6 2.5 39 42-85 95-133 (147)
14 PF13909 zf-H2C2_5: C2H2-type 88.4 0.32 7E-06 27.0 1.5 24 47-70 1-24 (24)
15 PHA00732 hypothetical protein 87.8 0.62 1.4E-05 33.8 3.1 42 47-93 2-44 (79)
16 PF08271 TF_Zn_Ribbon: TFIIB z 87.5 0.19 4.2E-06 32.0 0.2 34 47-90 1-34 (43)
17 PHA00733 hypothetical protein 87.3 0.95 2.1E-05 35.3 4.1 50 45-98 72-124 (128)
18 PLN03208 E3 ubiquitin-protein 86.8 0.37 8E-06 40.8 1.6 45 44-88 16-81 (193)
19 PF14354 Lar_restr_allev: Rest 85.1 0.17 3.7E-06 33.8 -1.0 31 46-83 3-37 (61)
20 smart00834 CxxC_CXXC_SSSS Puta 84.9 0.2 4.4E-06 30.7 -0.6 33 45-85 4-36 (41)
21 TIGR01206 lysW lysine biosynth 84.6 0.29 6.2E-06 33.7 -0.1 30 46-84 2-31 (54)
22 PRK09710 lar restriction allev 84.3 0.31 6.8E-06 34.9 0.1 30 46-84 6-36 (64)
23 TIGR02098 MJ0042_CXXC MJ0042 f 84.0 0.7 1.5E-05 28.3 1.5 32 47-84 3-34 (38)
24 PHA02768 hypothetical protein; 83.5 1.1 2.5E-05 31.0 2.5 34 46-83 5-39 (55)
25 PLN03086 PRLI-interacting fact 83.0 1.2 2.7E-05 43.0 3.5 38 45-85 477-514 (567)
26 PF12756 zf-C2H2_2: C2H2 type 82.0 0.85 1.9E-05 31.5 1.5 26 45-70 49-75 (100)
27 smart00734 ZnF_Rad18 Rad18-lik 81.1 1.5 3.2E-05 25.8 2.1 20 47-66 2-21 (26)
28 PRK14892 putative transcriptio 79.0 0.7 1.5E-05 35.3 0.3 34 43-85 18-52 (99)
29 smart00504 Ubox Modified RING 78.5 2.7 5.8E-05 27.5 3.0 27 53-86 20-46 (63)
30 TIGR02605 CxxC_CxxC_SSSS putat 77.8 0.91 2E-05 29.5 0.5 32 45-84 4-35 (52)
31 KOG1842 FYVE finger-containing 76.4 1.6 3.4E-05 41.7 1.8 33 42-74 11-44 (505)
32 smart00355 ZnF_C2H2 zinc finge 76.0 3.8 8.3E-05 21.4 2.6 23 47-70 1-24 (26)
33 PF08274 PhnA_Zn_Ribbon: PhnA 75.5 0.89 1.9E-05 27.9 -0.0 24 48-83 4-27 (30)
34 PF14255 Cys_rich_CPXG: Cystei 74.9 1.2 2.5E-05 30.4 0.4 12 47-58 1-12 (52)
35 PF05605 zf-Di19: Drought indu 74.4 2.7 5.9E-05 27.7 2.1 24 46-70 31-54 (54)
36 PHA00616 hypothetical protein 73.7 2.1 4.6E-05 28.4 1.4 26 47-72 2-28 (44)
37 PTZ00255 60S ribosomal protein 73.4 1 2.2E-05 34.1 -0.2 17 41-57 31-48 (90)
38 cd00350 rubredoxin_like Rubred 73.2 1.3 2.8E-05 27.0 0.3 25 47-84 2-26 (33)
39 PRK00398 rpoP DNA-directed RNA 72.9 1.7 3.7E-05 27.9 0.8 28 46-84 3-30 (46)
40 PF05129 Elf1: Transcription e 72.3 1.6 3.5E-05 31.9 0.7 35 43-84 19-55 (81)
41 PF03470 zf-XS: XS zinc finger 72.2 2.7 5.9E-05 27.9 1.7 9 78-86 1-9 (43)
42 PF14206 Cys_rich_CPCC: Cystei 70.1 1.8 4E-05 31.8 0.5 27 46-83 1-28 (78)
43 PF12773 DZR: Double zinc ribb 69.6 2.7 6E-05 26.9 1.2 28 47-86 13-40 (50)
44 KOG2462 C2H2-type Zn-finger pr 69.5 3.6 7.8E-05 36.8 2.3 85 44-139 159-275 (279)
45 PF13912 zf-C2H2_6: C2H2-type 69.1 2.7 6E-05 23.5 1.0 24 46-69 1-25 (27)
46 TIGR00373 conserved hypothetic 68.3 5.6 0.00012 32.0 3.0 34 42-85 105-138 (158)
47 KOG2593 Transcription initiati 68.0 3 6.6E-05 39.3 1.7 64 33-103 115-192 (436)
48 PF07754 DUF1610: Domain of un 67.6 3 6.6E-05 24.5 1.0 12 43-54 13-24 (24)
49 TIGR00280 L37a ribosomal prote 67.4 1.5 3.2E-05 33.3 -0.4 17 41-57 30-47 (91)
50 cd00729 rubredoxin_SM Rubredox 66.9 2.1 4.6E-05 26.5 0.3 26 46-84 2-27 (34)
51 PF04780 DUF629: Protein of un 66.9 5.4 0.00012 37.9 3.1 41 44-84 55-99 (466)
52 TIGR03655 anti_R_Lar restricti 66.8 2.5 5.5E-05 28.0 0.7 7 48-54 3-9 (53)
53 PRK03976 rpl37ae 50S ribosomal 66.1 1.7 3.6E-05 32.9 -0.4 17 41-57 31-48 (90)
54 PRK06266 transcription initiat 65.9 4.9 0.00011 33.0 2.3 34 42-85 113-146 (178)
55 PF02176 zf-TRAF: TRAF-type zi 63.7 1.9 4E-05 28.3 -0.5 45 46-92 9-60 (60)
56 KOG3623 Homeobox transcription 63.5 3.1 6.8E-05 42.1 0.9 40 45-84 209-249 (1007)
57 PF11789 zf-Nse: Zinc-finger o 63.3 5.7 0.00012 27.1 1.9 23 53-80 31-53 (57)
58 COG4888 Uncharacterized Zn rib 59.8 4.2 9E-05 31.7 0.8 37 43-84 19-55 (104)
59 PF13395 HNH_4: HNH endonuclea 59.7 5.1 0.00011 26.6 1.1 14 49-62 1-14 (54)
60 PRK14890 putative Zn-ribbon RN 59.6 7 0.00015 27.6 1.8 33 43-82 22-55 (59)
61 KOG0320 Predicted E3 ubiquitin 58.9 10 0.00022 32.3 3.0 44 44-87 129-179 (187)
62 smart00659 RPOLCX RNA polymera 58.4 5.1 0.00011 26.2 0.9 28 46-85 2-29 (44)
63 PF03145 Sina: Seven in absent 58.0 5.4 0.00012 32.4 1.2 54 45-101 13-75 (198)
64 PF04564 U-box: U-box domain; 57.0 11 0.00023 26.3 2.4 36 45-86 3-50 (73)
65 COG0675 Transposase and inacti 56.9 9.4 0.0002 31.4 2.5 47 33-95 296-342 (364)
66 PRK12495 hypothetical protein; 56.6 6.7 0.00015 34.2 1.6 28 45-85 41-68 (226)
67 KOG2462 C2H2-type Zn-finger pr 56.5 10 0.00022 34.0 2.8 59 43-102 127-189 (279)
68 COG2888 Predicted Zn-ribbon RN 55.1 11 0.00024 26.9 2.2 34 42-82 23-57 (61)
69 PF09723 Zn-ribbon_8: Zinc rib 54.5 3.2 6.9E-05 26.5 -0.5 31 45-83 4-34 (42)
70 PF07282 OrfB_Zn_ribbon: Putat 54.3 12 0.00027 25.2 2.4 48 32-92 15-63 (69)
71 PF14634 zf-RING_5: zinc-RING 54.1 11 0.00025 23.6 2.0 20 61-82 24-43 (44)
72 PF15616 TerY-C: TerY-C metal 52.6 3.4 7.4E-05 33.1 -0.7 40 47-88 78-118 (131)
73 PF10571 UPF0547: Uncharacteri 51.8 9.3 0.0002 22.5 1.2 8 49-56 3-10 (26)
74 COG4311 SoxD Sarcosine oxidase 51.0 7 0.00015 30.1 0.7 9 46-54 3-11 (97)
75 COG5175 MOT2 Transcriptional r 49.0 12 0.00026 35.2 2.1 35 49-84 17-62 (480)
76 PRK00420 hypothetical protein; 48.6 13 0.00029 29.0 2.0 27 47-85 24-50 (112)
77 PF13465 zf-H2C2_2: Zinc-finge 48.3 17 0.00037 20.7 1.9 22 60-83 1-22 (26)
78 PF01780 Ribosomal_L37ae: Ribo 48.3 7.3 0.00016 29.5 0.5 13 42-54 31-43 (90)
79 cd00730 rubredoxin Rubredoxin; 47.1 10 0.00022 25.6 1.0 13 42-54 30-42 (50)
80 PF14446 Prok-RING_1: Prokaryo 46.9 13 0.00028 25.8 1.5 25 47-84 6-30 (54)
81 COG5415 Predicted integral mem 46.8 16 0.00035 32.1 2.4 35 42-85 188-224 (251)
82 PF13719 zinc_ribbon_5: zinc-r 46.4 17 0.00037 22.6 1.9 31 47-83 3-33 (37)
83 PRK00423 tfb transcription ini 45.6 12 0.00027 32.8 1.6 38 45-93 10-48 (310)
84 TIGR00100 hypA hydrogenase nic 45.4 6.4 0.00014 30.1 -0.2 30 42-84 66-95 (115)
85 PF12171 zf-C2H2_jaz: Zinc-fin 45.3 14 0.00031 20.9 1.3 21 47-67 2-23 (27)
86 PF14616 DUF4451: Domain of un 45.3 14 0.0003 28.8 1.6 29 75-103 25-58 (124)
87 smart00451 ZnF_U1 U1-like zinc 45.0 18 0.00038 21.1 1.7 23 46-68 3-26 (35)
88 PRK03922 hypothetical protein; 44.6 11 0.00024 29.8 1.0 14 46-59 49-62 (113)
89 PF13248 zf-ribbon_3: zinc-rib 44.5 15 0.00032 21.2 1.3 9 48-56 4-12 (26)
90 PF00097 zf-C3HC4: Zinc finger 44.1 3 6.5E-05 25.3 -1.8 9 73-81 33-41 (41)
91 PF04475 DUF555: Protein of un 43.9 11 0.00025 29.2 1.0 14 46-59 47-60 (102)
92 PF04423 Rad50_zn_hook: Rad50 43.1 9.5 0.00021 25.2 0.4 14 48-61 22-35 (54)
93 PF02892 zf-BED: BED zinc fing 42.7 13 0.00028 23.1 0.9 25 45-69 15-44 (45)
94 PF08996 zf-DNA_Pol: DNA Polym 42.1 3 6.5E-05 34.2 -2.6 39 45-85 17-55 (188)
95 KOG0402 60S ribosomal protein 41.8 7.8 0.00017 29.5 -0.2 15 42-56 32-47 (92)
96 PF04981 NMD3: NMD3 family ; 41.5 16 0.00035 30.8 1.6 36 49-84 1-44 (236)
97 PF00301 Rubredoxin: Rubredoxi 40.5 13 0.00029 24.7 0.8 13 42-54 30-42 (47)
98 PF08209 Sgf11: Sgf11 (transcr 40.4 21 0.00046 22.3 1.6 20 74-93 3-23 (33)
99 COG1997 RPL43A Ribosomal prote 40.2 6 0.00013 30.0 -1.0 16 39-54 28-43 (89)
100 PF13824 zf-Mss51: Zinc-finger 39.8 16 0.00036 25.3 1.2 13 42-54 10-22 (55)
101 COG1592 Rubrerythrin [Energy p 39.6 16 0.00034 30.3 1.2 25 46-84 134-158 (166)
102 PRK12496 hypothetical protein; 39.5 21 0.00046 28.9 1.9 28 46-86 127-154 (164)
103 PF10058 DUF2296: Predicted in 39.4 16 0.00034 24.9 1.0 10 45-54 43-52 (54)
104 PRK11088 rrmA 23S rRNA methylt 39.4 6.2 0.00013 33.2 -1.2 26 46-71 2-27 (272)
105 KOG0823 Predicted E3 ubiquitin 39.3 14 0.00029 32.4 0.8 44 44-88 45-97 (230)
106 KOG2177 Predicted E3 ubiquitin 38.4 13 0.00029 28.8 0.6 37 45-83 12-55 (386)
107 KOG3608 Zn finger proteins [Ge 38.0 38 0.00083 32.0 3.6 49 45-94 262-313 (467)
108 smart00614 ZnF_BED BED zinc fi 37.9 19 0.00041 23.4 1.2 26 45-70 17-48 (50)
109 TIGR00570 cdk7 CDK-activating 37.0 26 0.00056 31.8 2.3 39 46-85 3-53 (309)
110 smart00507 HNHc HNH nucleases. 36.8 4.7 0.0001 24.3 -1.8 21 47-67 11-31 (52)
111 PF12760 Zn_Tnp_IS1595: Transp 36.7 20 0.00043 23.0 1.1 11 44-54 16-26 (46)
112 KOG2932 E3 ubiquitin ligase in 36.6 16 0.00035 33.8 0.9 58 46-103 90-177 (389)
113 COG1281 Disulfide bond chapero 36.5 10 0.00023 33.9 -0.3 18 43-60 263-282 (286)
114 PF09538 FYDLN_acid: Protein o 36.1 20 0.00044 27.5 1.3 28 45-85 8-36 (108)
115 PHA00733 hypothetical protein 36.1 35 0.00075 26.6 2.6 25 46-70 99-124 (128)
116 PF07191 zinc-ribbons_6: zinc- 35.9 1.2 2.5E-05 32.4 -5.2 52 48-103 3-61 (70)
117 PRK11595 DNA utilization prote 35.8 19 0.0004 30.1 1.1 21 48-68 7-29 (227)
118 PF14353 CpXC: CpXC protein 35.5 16 0.00036 27.6 0.7 29 44-76 36-64 (128)
119 PRK12380 hydrogenase nickel in 35.3 12 0.00026 28.5 -0.1 30 42-84 66-95 (113)
120 PF09986 DUF2225: Uncharacteri 34.9 16 0.00035 30.6 0.6 17 46-62 5-21 (214)
121 PHA02929 N1R/p28-like protein; 34.9 19 0.00041 31.3 1.1 42 44-85 172-226 (238)
122 TIGR00373 conserved hypothetic 34.6 28 0.0006 28.0 1.9 21 45-65 127-150 (158)
123 PF04780 DUF629: Protein of un 33.7 20 0.00044 34.1 1.1 47 56-102 21-86 (466)
124 COG3326 Predicted membrane pro 33.2 35 0.00077 26.1 2.1 30 106-148 31-62 (94)
125 TIGR00686 phnA alkylphosphonat 33.1 18 0.00038 28.5 0.5 13 72-84 16-28 (109)
126 PF02146 SIR2: Sir2 family; I 33.0 16 0.00035 29.0 0.3 41 45-90 104-144 (178)
127 COG4391 Uncharacterized protei 32.6 21 0.00045 25.5 0.8 13 72-84 45-57 (62)
128 PF05207 zf-CSL: CSL zinc fing 32.5 14 0.00029 25.1 -0.2 45 33-86 4-51 (55)
129 PF03966 Trm112p: Trm112p-like 32.5 26 0.00056 24.1 1.2 39 45-83 6-61 (68)
130 TIGR01374 soxD sarcosine oxida 32.2 20 0.00044 26.8 0.7 8 47-54 2-9 (84)
131 PF14447 Prok-RING_4: Prokaryo 32.2 23 0.00049 24.7 0.9 13 46-58 39-51 (55)
132 KOG4628 Predicted E3 ubiquitin 32.1 9.2 0.0002 35.1 -1.4 40 46-85 229-277 (348)
133 PRK03824 hypA hydrogenase nick 32.0 16 0.00035 28.7 0.1 43 42-84 66-116 (135)
134 PF12660 zf-TFIIIC: Putative z 31.8 8.2 0.00018 28.9 -1.5 38 48-85 16-65 (99)
135 cd03019 DsbA_DsbA DsbA family, 31.7 19 0.00041 27.3 0.5 19 45-63 23-42 (178)
136 COG4049 Uncharacterized protei 31.6 26 0.00056 25.0 1.1 26 76-101 18-45 (65)
137 PF08368 FAST_2: FAST kinase-l 31.3 23 0.00049 25.8 0.8 28 122-150 48-75 (93)
138 KOG2817 Predicted E3 ubiquitin 31.0 27 0.00058 32.8 1.4 15 45-59 373-387 (394)
139 PRK05477 gatB aspartyl/glutamy 30.9 18 0.00038 34.4 0.2 21 65-85 27-47 (474)
140 PF14968 CCDC84: Coiled coil p 30.8 25 0.00054 32.2 1.1 26 41-66 53-85 (336)
141 PF06957 COPI_C: Coatomer (COP 30.4 16 0.00035 34.3 -0.1 34 45-91 379-413 (422)
142 COG5189 SFP1 Putative transcri 29.7 26 0.00056 32.7 1.0 40 46-85 349-408 (423)
143 PF13717 zinc_ribbon_4: zinc-r 29.7 43 0.00093 20.8 1.8 31 47-83 3-33 (36)
144 COG1675 TFA1 Transcription ini 29.0 32 0.00069 28.8 1.4 31 43-85 110-142 (176)
145 KOG1002 Nucleotide excision re 28.9 41 0.00089 33.5 2.3 56 38-93 528-593 (791)
146 COG1499 NMD3 NMD protein affec 28.8 33 0.00071 31.5 1.6 41 44-84 4-52 (355)
147 COG3058 FdhE Uncharacterized p 28.8 19 0.00042 32.6 0.1 18 74-91 184-201 (308)
148 KOG3940 Uncharacterized conser 28.6 34 0.00075 31.5 1.6 26 39-64 13-38 (351)
149 KOG1493 Anaphase-promoting com 27.7 62 0.0013 24.4 2.6 35 48-83 33-78 (84)
150 PF12874 zf-met: Zinc-finger o 27.5 37 0.0008 18.4 1.1 19 47-65 1-20 (25)
151 PF09706 Cas_CXXC_CXXC: CRISPR 27.4 20 0.00044 25.2 -0.0 11 44-54 3-13 (69)
152 PF12230 PRP21_like_P: Pre-mRN 27.4 21 0.00044 29.8 0.0 22 46-67 168-189 (229)
153 PF12013 DUF3505: Protein of u 27.0 47 0.001 24.5 1.9 36 72-107 8-44 (109)
154 PF11672 DUF3268: Protein of u 26.8 23 0.00049 27.3 0.1 38 47-87 3-43 (102)
155 PF10609 ParA: ParA/MinD ATPas 26.8 23 0.0005 26.1 0.2 14 42-55 61-74 (81)
156 PF01155 HypA: Hydrogenase exp 26.6 14 0.0003 28.0 -1.0 29 43-84 67-95 (113)
157 PF11290 DUF3090: Protein of u 26.4 34 0.00074 28.7 1.1 13 47-59 155-167 (171)
158 PF14369 zf-RING_3: zinc-finge 26.3 32 0.00068 21.4 0.7 9 48-56 23-31 (35)
159 PF08168 NUC205: NUC205 domain 26.3 22 0.00049 23.8 0.0 10 162-171 26-35 (44)
160 PLN02751 glutamyl-tRNA(Gln) am 26.3 23 0.00051 34.3 0.2 21 65-85 83-103 (544)
161 TIGR02300 FYDLN_acid conserved 26.3 37 0.00081 27.4 1.3 31 43-86 6-37 (129)
162 KOG4696 Uncharacterized conser 26.2 48 0.001 30.7 2.1 26 46-72 2-27 (393)
163 PF13462 Thioredoxin_4: Thiore 26.2 6.4 0.00014 29.3 -2.9 21 45-65 20-41 (162)
164 PF04267 SoxD: Sarcosine oxida 25.9 18 0.00039 27.0 -0.6 7 48-54 3-9 (84)
165 KOG2231 Predicted E3 ubiquitin 25.4 47 0.001 33.2 2.0 29 44-72 180-209 (669)
166 KOG2879 Predicted E3 ubiquitin 24.7 22 0.00048 32.2 -0.3 41 45-85 238-286 (298)
167 PF03604 DNA_RNApol_7kD: DNA d 24.2 45 0.00098 20.6 1.1 13 42-54 13-25 (32)
168 PRK10220 hypothetical protein; 24.1 50 0.0011 26.1 1.6 12 73-84 18-29 (111)
169 TIGR00133 gatB glutamyl-tRNA(G 24.1 28 0.0006 33.1 0.2 14 72-85 34-47 (478)
170 COG5109 Uncharacterized conser 23.9 33 0.00072 31.9 0.7 10 45-54 375-384 (396)
171 cd02972 DsbA_family DsbA famil 23.6 22 0.00048 23.3 -0.4 17 46-62 6-23 (98)
172 PRK00564 hypA hydrogenase nick 23.6 28 0.00062 26.7 0.2 30 43-84 68-97 (117)
173 PRK00114 hslO Hsp33-like chape 23.5 20 0.00044 31.4 -0.8 49 32-84 221-277 (293)
174 KOG3576 Ovo and related transc 23.3 47 0.001 29.4 1.4 47 47-95 146-195 (267)
175 PRK03681 hypA hydrogenase nick 23.3 25 0.00053 26.9 -0.2 11 44-54 68-78 (114)
176 KOG0429 Ubiquitin-conjugating 22.9 31 0.00067 30.5 0.3 18 141-158 87-104 (258)
177 COG1656 Uncharacterized conser 22.7 62 0.0013 27.0 2.0 37 48-84 99-139 (165)
178 PF11793 FANCL_C: FANCL C-term 22.6 56 0.0012 22.8 1.5 46 42-87 16-67 (70)
179 PF10276 zf-CHCC: Zinc-finger 22.5 42 0.00091 21.7 0.8 9 46-54 29-37 (40)
180 PF09889 DUF2116: Uncharacteri 22.4 60 0.0013 22.7 1.6 10 48-57 5-14 (59)
181 PRK09678 DNA-binding transcrip 22.0 43 0.00092 24.2 0.8 8 47-54 2-9 (72)
182 PF04551 GcpE: GcpE protein; 21.9 48 0.001 30.8 1.3 25 46-70 268-293 (359)
183 PRK04023 DNA polymerase II lar 21.7 46 0.001 35.0 1.2 37 45-85 637-673 (1121)
184 COG1405 SUA7 Transcription ini 21.2 47 0.001 29.5 1.0 42 47-99 2-44 (285)
185 KOG3993 Transcription factor ( 20.3 28 0.00062 33.4 -0.5 33 45-77 457-490 (500)
186 COG1198 PriA Primosomal protei 20.0 38 0.00082 34.0 0.2 40 43-84 441-484 (730)
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=99.81 E-value=1.8e-20 Score=125.53 Aligned_cols=54 Identities=48% Similarity=0.938 Sum_probs=52.1
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccchhhHHhhhhhccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHG 98 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s~d~l~HL~~qH~ 98 (171)
++|+||||+++||+.+|++|+.++|+.+.++||||||+.+++.||++||+.+|+
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 379999999999999999999999999999999999999999999999999996
No 2
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=99.15 E-value=9.5e-12 Score=94.62 Aligned_cols=37 Identities=41% Similarity=0.533 Sum_probs=34.2
Q ss_pred hHhhhhhhhhhhhhhHHhcCc--------chhhhhhhhhhhcCCc
Q 030808 119 ALSLLGRDLREAHLQVLLGVL--------KILVQKVLHQHICGKQ 155 (171)
Q Consensus 119 ~ls~L~k~lre~~lq~llgg~--------s~~~~~~~~~~~~~~~ 155 (171)
|||+|||||||||||+||||+ ..+.||+|++||||--
T Consensus 1 tlsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~ 45 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFP 45 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCC
Confidence 689999999999999999998 5788999999999864
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.76 E-value=5.6e-09 Score=94.23 Aligned_cols=72 Identities=21% Similarity=0.433 Sum_probs=59.3
Q ss_pred ccchhhc-cCCCcCCCCCCCCCcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccccc---------hhhHHhhh
Q 030808 25 QSSQIDR-LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV---------ARDMLSHI 93 (171)
Q Consensus 25 ~~s~~~~-~g~e~~~~ddd~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~---------s~d~l~HL 93 (171)
.+-||++ ||+|-+..+++. .|+||||++ +|++..+.+|+..+|+..+..+|||||++.+ ..+...|+
T Consensus 59 ~~~dfeL~f~Ge~i~~y~~q--SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~~qp~~~~~~~~~~~~~ 136 (381)
T KOG1280|consen 59 SRVDFELYFGGEPISHYDPQ--SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPEMQPIHSKETENLSVHW 136 (381)
T ss_pred eccceeeEecCccccccccc--cccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcccCchhhhhhhhhhhhh
Confidence 3457777 788888776655 999999999 9999999999999999999999999999985 44555666
Q ss_pred hhccc
Q 030808 94 TLQHG 98 (171)
Q Consensus 94 ~~qH~ 98 (171)
+..|.
T Consensus 137 ~~~a~ 141 (381)
T KOG1280|consen 137 TEIAL 141 (381)
T ss_pred hhhcc
Confidence 55554
No 4
>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=94.71 E-value=0.025 Score=30.26 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=17.6
Q ss_pred ccCCCCCC-CCCHHHHHHhhhhhh
Q 030808 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (171)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~eeH 69 (171)
|.||+|+. --+..+|..|+...|
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 68999999 777888999988776
No 5
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.55 E-value=0.016 Score=41.68 Aligned_cols=45 Identities=33% Similarity=0.771 Sum_probs=30.7
Q ss_pred cCCCcCC-CCCCCCCcccCCCCCC--CCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 32 LSIDDFE-VEDDVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 32 ~g~e~~~-~ddd~r~~F~CPfC~e--~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
.-++|++ .+|...-+|+|| ||. .+....|. ..-..++||-|+-.+
T Consensus 7 Veiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 7 VEIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLII 54 (67)
T ss_pred EEeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEE
Confidence 4567777 444556789999 888 44444443 345678999999875
No 6
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.14 E-value=0.021 Score=40.82 Aligned_cols=45 Identities=31% Similarity=0.775 Sum_probs=29.5
Q ss_pred cCCCcCCCC-CCCCCcccCCCCCC--CCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 32 LSIDDFEVE-DDVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 32 ~g~e~~~~d-dd~r~~F~CPfC~e--~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
+.++|++-+ +++.-+|+|| ||. ++....|. ..-..++||-|+-++
T Consensus 7 ieiedftf~~e~~~ftyPCP-CGDRFeIsLeDl~--------~GE~VArCPSCSLiv 54 (67)
T COG5216 7 IEIEDFTFSREEKTFTYPCP-CGDRFEISLEDLR--------NGEVVARCPSCSLIV 54 (67)
T ss_pred eEeeeeEEcCCCceEEecCC-CCCEeEEEHHHhh--------CCceEEEcCCceEEE
Confidence 334444322 3456799999 777 55555553 345678999999886
No 7
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.50 E-value=0.068 Score=31.08 Aligned_cols=21 Identities=33% Similarity=0.668 Sum_probs=18.9
Q ss_pred cccCCCCCCCCCHHHHHHhhh
Q 030808 46 DFPCPYCYEDFDIASLCSHLE 66 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~ 66 (171)
..+||+|+..|....|-.|..
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 8
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=92.85 E-value=0.056 Score=37.53 Aligned_cols=27 Identities=26% Similarity=0.738 Sum_probs=18.8
Q ss_pred CCccccCCccccc--hhhHHhhhhhcccc
Q 030808 73 SKVTVCPICSVKV--ARDMLSHITLQHGH 99 (171)
Q Consensus 73 ~k~vVCPVCaa~~--s~d~l~HL~~qH~~ 99 (171)
.....||+|.+.+ ++|+-+||-+.|+.
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 4467899999886 78999999999964
No 9
>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=92.51 E-value=0.079 Score=28.93 Aligned_cols=21 Identities=24% Similarity=0.550 Sum_probs=16.5
Q ss_pred ccCCCCCC-CCCHHHHHHhhhh
Q 030808 47 FPCPYCYE-DFDIASLCSHLED 67 (171)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~e 67 (171)
|.||.|++ =-+...|..|+..
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 67899988 5567788888876
No 10
>PLN03086 PRLI-interacting factor K; Provisional
Probab=92.37 E-value=0.16 Score=48.98 Aligned_cols=48 Identities=23% Similarity=0.501 Sum_probs=38.1
Q ss_pred CCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc-chhhHHhhhhhc
Q 030808 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK-VARDMLSHITLQ 96 (171)
Q Consensus 44 r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~-~s~d~l~HL~~q 96 (171)
..-+.||+|++.|....|-.|....| +.+.|| |... ...++..|++..
T Consensus 451 ~~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~th 499 (567)
T PLN03086 451 KNHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQAST 499 (567)
T ss_pred ccCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhcc
Confidence 34578999999999999999999866 678999 9644 456888887643
No 11
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.79 E-value=0.12 Score=48.01 Aligned_cols=89 Identities=25% Similarity=0.343 Sum_probs=60.1
Q ss_pred CcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCcccc--------------------------------------c
Q 030808 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK--------------------------------------V 85 (171)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~--------------------------------------~ 85 (171)
--=.|-||.. =+|-.+|..||...|- .|-||..+ +
T Consensus 219 GHP~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~ 292 (493)
T COG5236 219 GHPLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFP 292 (493)
T ss_pred CCchhhhccceecChHHHHHHHHhhhh------hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEec
Confidence 3457999999 8899999999999986 45555443 1
Q ss_pred -hhhHHhhhhhcccchhhhhhhcccccCCCCCchhHhhhhhhhhhhhhhHH--hcCcchh
Q 030808 86 -ARDMLSHITLQHGHLFKLQRRRRLRRVAIPSSQALSLLGRDLREAHLQVL--LGVLKIL 142 (171)
Q Consensus 86 -s~d~l~HL~~qH~~~~k~~r~rr~rr~~~ps~s~ls~L~k~lre~~lq~l--lgg~s~~ 142 (171)
-..++.||+..|+...+.+-+-+-.+-++|-+.- ..++-.++.|-++ +||+++.
T Consensus 293 ~~~el~~h~~~~h~~~~~~~~~~~~~~~s~~i~~p---~~r~~~~~~~~~i~~~~g~~~~ 349 (493)
T COG5236 293 YHTELLEHLTRFHKVNARLSEIPRPGRCSIPVMDP---FKRKKAPARVSVIDPSGGNARA 349 (493)
T ss_pred cHHHHHHHHHHHhhcccccCcCCCCccccccccch---hhhccCcccCccccCCCCCCCC
Confidence 3468999999999998765443333334443222 3444446666666 6777654
No 12
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.17 E-value=0.16 Score=35.19 Aligned_cols=48 Identities=21% Similarity=0.529 Sum_probs=15.1
Q ss_pred CCCCCC-CCCHHHHHHhhhhhhcCCCC---------------------ccccCCccccc--hhhHHhhhhhc
Q 030808 49 CPYCYE-DFDIASLCSHLEDEHSCESK---------------------VTVCPICSVKV--ARDMLSHITLQ 96 (171)
Q Consensus 49 CPfC~e-~fD~~~L~~H~~eeH~~e~k---------------------~vVCPVCaa~~--s~d~l~HL~~q 96 (171)
|+||+. -=+...|..|+...|.+... .-.|++|.... ...+..||...
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -----------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 999999 45688999999999986322 13499998875 56888999754
No 13
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.50 E-value=0.29 Score=38.60 Aligned_cols=39 Identities=18% Similarity=0.516 Sum_probs=27.0
Q ss_pred CCCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
.....|.||.|+..|+..+-..... .....+||.|-..+
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d-----~~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLD-----MDGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcC-----CCCcEECCCCCCEE
Confidence 4567999999999666544333222 13458999998876
No 14
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=88.44 E-value=0.32 Score=26.96 Aligned_cols=24 Identities=29% Similarity=0.635 Sum_probs=16.7
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhc
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHS 70 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~ 70 (171)
|.||+|.-.-....|..|++..|+
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 679999872238889999888774
No 15
>PHA00732 hypothetical protein
Probab=87.75 E-value=0.62 Score=33.84 Aligned_cols=42 Identities=29% Similarity=0.652 Sum_probs=31.6
Q ss_pred ccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccccchhhHHhhh
Q 030808 47 FPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (171)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s~d~l~HL 93 (171)
|.|+.|++ --+...|..|....|.. ..|++|...-. ++..|+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~-~l~~H~ 44 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR-RLNQHF 44 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC-Chhhhh
Confidence 78999999 44788899998866653 26999977644 466666
No 16
>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=87.48 E-value=0.19 Score=32.02 Aligned_cols=34 Identities=26% Similarity=0.616 Sum_probs=21.1
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccchhhHH
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s~d~l 90 (171)
|.||.|+... + .. -.+....||+.|-..+..+.+
T Consensus 1 m~Cp~Cg~~~-~------~~---D~~~g~~vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VF---DPERGELVCPNCGLVLEENII 34 (43)
T ss_dssp ESBTTTSSSE-E------EE---ETTTTEEEETTT-BBEE-TTB
T ss_pred CCCcCCcCCc-e------EE---cCCCCeEECCCCCCEeecccc
Confidence 6799998832 1 11 144567899999887765543
No 17
>PHA00733 hypothetical protein
Probab=87.34 E-value=0.95 Score=35.33 Aligned_cols=50 Identities=26% Similarity=0.603 Sum_probs=36.7
Q ss_pred CcccCCCCCCC-CCHHHHHHhhhhhhcCCCCccccCCcccc--chhhHHhhhhhccc
Q 030808 45 PDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVK--VARDMLSHITLQHG 98 (171)
Q Consensus 45 ~~F~CPfC~e~-fD~~~L~~H~~eeH~~e~k~vVCPVCaa~--~s~d~l~HL~~qH~ 98 (171)
..|.|+.|++. -....|..|... | .....|++|... ...++..|+..-|+
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 46999999995 456678888874 2 234699999765 36688888877775
No 18
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=86.84 E-value=0.37 Score=40.81 Aligned_cols=45 Identities=24% Similarity=0.697 Sum_probs=28.1
Q ss_pred CCcccCCCCCCCCC--HHHHHHh-----hhhhhcC--------------CCCccccCCccccchhh
Q 030808 44 RPDFPCPYCYEDFD--IASLCSH-----LEDEHSC--------------ESKVTVCPICSVKVARD 88 (171)
Q Consensus 44 r~~F~CPfC~e~fD--~~~L~~H-----~~eeH~~--------------e~k~vVCPVCaa~~s~d 88 (171)
...|.||.|.+.+. +...|.| |-.+... ..+...||+|...++.+
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~ 81 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA 81 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence 45799999988332 3445666 3433211 23456899999988653
No 19
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=85.11 E-value=0.17 Score=33.84 Aligned_cols=31 Identities=26% Similarity=0.590 Sum_probs=19.6
Q ss_pred cccCCCCCC-CCCHHHHHHhhhhhhcCCC---CccccCCccc
Q 030808 46 DFPCPYCYE-DFDIASLCSHLEDEHSCES---KVTVCPICSV 83 (171)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~---k~vVCPVCaa 83 (171)
.-+|||||. .+.+.. ....+. -.|.|..|.+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 468999987 554433 222222 4577999977
No 20
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=84.86 E-value=0.2 Score=30.72 Aligned_cols=33 Identities=21% Similarity=0.632 Sum_probs=22.3
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
.+|.||-||..|++..-. .+...++||.|.+.+
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 468999999976643211 225678899998743
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=84.61 E-value=0.29 Score=33.68 Aligned_cols=30 Identities=20% Similarity=0.686 Sum_probs=21.6
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
.|.||-|++.+++.... . .-.|.||.|.+.
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 58999999977654332 1 336899999876
No 22
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=84.33 E-value=0.31 Score=34.86 Aligned_cols=30 Identities=20% Similarity=0.473 Sum_probs=21.0
Q ss_pred cccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
.=+||||+. .+++. |....-.++|.-|.+.
T Consensus 6 lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVK---------AISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEE---------ecCceEEEEcCCCCcC
Confidence 458999999 66554 2333335999999886
No 23
>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=83.97 E-value=0.7 Score=28.34 Aligned_cols=32 Identities=19% Similarity=0.520 Sum_probs=19.3
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
+.||.|+..|.+..- ....+...+.||.|-..
T Consensus 3 ~~CP~C~~~~~v~~~------~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS------QLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHH------HcCCCCCEEECCCCCCE
Confidence 679999884443321 12233347889999654
No 24
>PHA02768 hypothetical protein; Provisional
Probab=83.49 E-value=1.1 Score=31.01 Aligned_cols=34 Identities=26% Similarity=0.529 Sum_probs=25.1
Q ss_pred cccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccc
Q 030808 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (171)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa 83 (171)
.|.||.||+ =...+.|..|... |. ++-.|..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~-H~---k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK-HN---TNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh-cC---CcccCCcccc
Confidence 488999999 5567789999988 44 3556666654
No 25
>PLN03086 PRLI-interacting factor K; Provisional
Probab=83.04 E-value=1.2 Score=43.00 Aligned_cols=38 Identities=18% Similarity=0.474 Sum_probs=24.1
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
..+.|| |+..+....|..|.. .|+. .+...|+.|...+
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~-thCp-~Kpi~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQA-STCP-LRLITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhh-ccCC-CCceeCCCCCCcc
Confidence 346777 777667777777764 3443 3566777776554
No 26
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=81.99 E-value=0.85 Score=31.54 Aligned_cols=26 Identities=35% Similarity=0.884 Sum_probs=21.2
Q ss_pred CcccCCCCCCCC-CHHHHHHhhhhhhc
Q 030808 45 PDFPCPYCYEDF-DIASLCSHLEDEHS 70 (171)
Q Consensus 45 ~~F~CPfC~e~f-D~~~L~~H~~eeH~ 70 (171)
..|.|++|++.| +..+|..|+...+.
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCccC
Confidence 369999999955 89999999998754
No 27
>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=81.10 E-value=1.5 Score=25.78 Aligned_cols=20 Identities=30% Similarity=0.796 Sum_probs=12.2
Q ss_pred ccCCCCCCCCCHHHHHHhhh
Q 030808 47 FPCPYCYEDFDIASLCSHLE 66 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~ 66 (171)
..||.|++.+....+-.|++
T Consensus 2 v~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVPENLINSHLD 21 (26)
T ss_pred CcCCCCcCcccHHHHHHHHH
Confidence 35666666666666666655
No 28
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=79.04 E-value=0.7 Score=35.27 Aligned_cols=34 Identities=18% Similarity=0.507 Sum_probs=21.3
Q ss_pred CCCcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 43 ~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
....|.||+|++ -+.+. -.+ ..-.++||+|-..-
T Consensus 18 lpt~f~CP~Cge~~v~v~-------~~k--~~~h~~C~~CG~y~ 52 (99)
T PRK14892 18 LPKIFECPRCGKVSISVK-------IKK--NIAIITCGNCGLYT 52 (99)
T ss_pred CCcEeECCCCCCeEeeee-------cCC--CcceEECCCCCCcc
Confidence 346899999996 22211 111 23458999998764
No 29
>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=78.55 E-value=2.7 Score=27.46 Aligned_cols=27 Identities=7% Similarity=0.113 Sum_probs=19.2
Q ss_pred CCCCCHHHHHHhhhhhhcCCCCccccCCccccch
Q 030808 53 YEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (171)
Q Consensus 53 ~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s 86 (171)
|.-|+...+.+++.. ...||+|....+
T Consensus 20 G~v~~~~~i~~~~~~-------~~~cP~~~~~~~ 46 (63)
T smart00504 20 GQTYERRAIEKWLLS-------HGTDPVTGQPLT 46 (63)
T ss_pred CCEEeHHHHHHHHHH-------CCCCCCCcCCCC
Confidence 445777888887765 358999987653
No 30
>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=77.83 E-value=0.91 Score=29.47 Aligned_cols=32 Identities=19% Similarity=0.702 Sum_probs=22.1
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
.+|.|+-|+..|++. .... +...+.||.|.+.
T Consensus 4 Yey~C~~Cg~~fe~~---~~~~-----~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 4 YEYRCTACGHRFEVL---QKMS-----DDPLATCPECGGE 35 (52)
T ss_pred EEEEeCCCCCEeEEE---EecC-----CCCCCCCCCCCCC
Confidence 479999999988743 1111 2456789999873
No 31
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=76.41 E-value=1.6 Score=41.69 Aligned_cols=33 Identities=33% Similarity=0.712 Sum_probs=28.5
Q ss_pred CCCCcccCCCCCCCC-CHHHHHHhhhhhhcCCCC
Q 030808 42 DVRPDFPCPYCYEDF-DIASLCSHLEDEHSCESK 74 (171)
Q Consensus 42 d~r~~F~CPfC~e~f-D~~~L~~H~~eeH~~e~k 74 (171)
+.+.-|.||+|.++| +...|-+|.+.+|..|..
T Consensus 11 ~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ed~ 44 (505)
T KOG1842|consen 11 EILEGFLCPICLLDLPNLSALNDHLDVEHFEEDE 44 (505)
T ss_pred hhhhcccCchHhhhhhhHHHHHHHHhhhccccch
Confidence 457789999999966 478899999999999875
No 32
>smart00355 ZnF_C2H2 zinc finger.
Probab=75.98 E-value=3.8 Score=21.40 Aligned_cols=23 Identities=26% Similarity=0.569 Sum_probs=16.2
Q ss_pred ccCCCCCC-CCCHHHHHHhhhhhhc
Q 030808 47 FPCPYCYE-DFDIASLCSHLEDEHS 70 (171)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~eeH~ 70 (171)
|.|+.|++ =-+...|..|.. .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 57888888 456667888876 553
No 33
>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=75.55 E-value=0.89 Score=27.92 Aligned_cols=24 Identities=29% Similarity=0.899 Sum_probs=12.5
Q ss_pred cCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccc
Q 030808 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (171)
Q Consensus 48 ~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa 83 (171)
.||.|+.++.. .+....|||-|..
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTTE
T ss_pred CCCCCCCccee------------ccCCEEeCCcccc
Confidence 58888775444 5677789999864
No 34
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=74.92 E-value=1.2 Score=30.44 Aligned_cols=12 Identities=50% Similarity=1.270 Sum_probs=9.0
Q ss_pred ccCCCCCCCCCH
Q 030808 47 FPCPYCYEDFDI 58 (171)
Q Consensus 47 F~CPfC~e~fD~ 58 (171)
+.|||||+.+++
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 479999995543
No 35
>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=74.42 E-value=2.7 Score=27.74 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=20.3
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhc
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHS 70 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~ 70 (171)
.+.||.|...+.. .|..|+...|+
T Consensus 31 ~v~CPiC~~~~~~-~l~~Hl~~~H~ 54 (54)
T PF05605_consen 31 NVVCPICSSRVTD-NLIRHLNSQHR 54 (54)
T ss_pred CccCCCchhhhhh-HHHHHHHHhcC
Confidence 6999999986653 99999998884
No 36
>PHA00616 hypothetical protein
Probab=73.70 E-value=2.1 Score=28.44 Aligned_cols=26 Identities=19% Similarity=0.268 Sum_probs=21.1
Q ss_pred ccCCCCCC-CCCHHHHHHhhhhhhcCC
Q 030808 47 FPCPYCYE-DFDIASLCSHLEDEHSCE 72 (171)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~eeH~~e 72 (171)
|.||-||. =....+|..|+...|.-+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~ 28 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQN 28 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCC
Confidence 78999999 667788999998877753
No 37
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=73.36 E-value=1 Score=34.13 Aligned_cols=17 Identities=18% Similarity=0.610 Sum_probs=13.5
Q ss_pred CCCCCcccCCCCCC-CCC
Q 030808 41 DDVRPDFPCPYCYE-DFD 57 (171)
Q Consensus 41 dd~r~~F~CPfC~e-~fD 57 (171)
..+.+.|+||||+. .+.
T Consensus 31 ~~q~a~y~CpfCgk~~vk 48 (90)
T PTZ00255 31 ISQHAKYFCPFCGKHAVK 48 (90)
T ss_pred HHHhCCccCCCCCCCcee
Confidence 36788999999987 554
No 38
>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=73.25 E-value=1.3 Score=26.99 Aligned_cols=25 Identities=32% Similarity=0.788 Sum_probs=14.8
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
|.|+.||.-+|... ..-+||+|.+.
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCCc
Confidence 56777776333222 45578888653
No 39
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.90 E-value=1.7 Score=27.91 Aligned_cols=28 Identities=18% Similarity=0.719 Sum_probs=16.0
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
+|.||-||..++.... ...+.||.|...
T Consensus 3 ~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEY-----------GTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCC-----------CCceECCCCCCe
Confidence 5777777775544110 115677777654
No 40
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=72.30 E-value=1.6 Score=31.88 Aligned_cols=35 Identities=20% Similarity=0.600 Sum_probs=14.2
Q ss_pred CCCcccCCCCC-C-CCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 43 VRPDFPCPYCY-E-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 43 ~r~~F~CPfC~-e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
+...|.||||+ + .+.+. -.-....-.+.|-+|-..
T Consensus 19 l~~~F~CPfC~~~~sV~v~-------idkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVK-------IDKKEGIGILSCRVCGES 55 (81)
T ss_dssp -SS----TTT--SS-EEEE-------EETTTTEEEEEESSS--E
T ss_pred CCceEcCCcCCCCCeEEEE-------EEccCCEEEEEecCCCCe
Confidence 34689999998 4 33221 111233345789999654
No 41
>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=72.20 E-value=2.7 Score=27.94 Aligned_cols=9 Identities=44% Similarity=1.102 Sum_probs=4.3
Q ss_pred cCCccccch
Q 030808 78 CPICSVKVA 86 (171)
Q Consensus 78 CPVCaa~~s 86 (171)
||.|..+..
T Consensus 1 CP~C~~kkk 9 (43)
T PF03470_consen 1 CPFCPGKKK 9 (43)
T ss_pred CCCCCCCCC
Confidence 455554443
No 42
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=70.09 E-value=1.8 Score=31.80 Aligned_cols=27 Identities=30% Similarity=0.898 Sum_probs=18.4
Q ss_pred cccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccc
Q 030808 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (171)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa 83 (171)
.|+||-||. -|+..+ +...-+||||-=
T Consensus 1 K~~CPCCg~~Tl~~~~-----------~~~ydIC~VC~W 28 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERG-----------EGTYDICPVCFW 28 (78)
T ss_pred CccCCCCCcEEeccCC-----------CcCceECCCCCc
Confidence 379999988 665432 223569999954
No 43
>PF12773 DZR: Double zinc ribbon
Probab=69.59 E-value=2.7 Score=26.89 Aligned_cols=28 Identities=21% Similarity=0.562 Sum_probs=19.4
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccch
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s 86 (171)
=.||.||..+. ..+...++||.|.+.+.
T Consensus 13 ~fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 13 KFCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred cCChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 35777777655 44556788999987653
No 44
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=69.50 E-value=3.6 Score=36.82 Aligned_cols=85 Identities=21% Similarity=0.395 Sum_probs=49.0
Q ss_pred CCcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCcccc----------------------------c--hhhHHhh
Q 030808 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK----------------------------V--ARDMLSH 92 (171)
Q Consensus 44 r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~----------------------------~--s~d~l~H 92 (171)
+..|.||+|++ -+..-.|--|+... . -.-+|+||-.. - -.|+-.|
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH-~---l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAH 234 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTH-T---LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAH 234 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhcc-C---CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHH
Confidence 56788888888 88888888887642 2 13345555443 1 3477777
Q ss_pred hhhcccc-hhhhhhhcccccCCCCCchhHhhhhhhhhhhhhhHHhcCc
Q 030808 93 ITLQHGH-LFKLQRRRRLRRVAIPSSQALSLLGRDLREAHLQVLLGVL 139 (171)
Q Consensus 93 L~~qH~~-~~k~~r~rr~rr~~~ps~s~ls~L~k~lre~~lq~llgg~ 139 (171)
|...=.. -|.. .+.-|.. +-+|+|-|-+..|=+..+.|+.
T Consensus 235 mQTHS~~K~~qC---~~C~KsF----sl~SyLnKH~ES~C~~~~~g~~ 275 (279)
T KOG2462|consen 235 MQTHSDVKKHQC---PRCGKSF----ALKSYLNKHSESACLKYLAGVM 275 (279)
T ss_pred HHhhcCCccccC---cchhhHH----HHHHHHHHhhhhccccccccCC
Confidence 7542211 1111 1223322 5678888887776665555554
No 45
>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=69.13 E-value=2.7 Score=23.49 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=17.4
Q ss_pred cccCCCCCC-CCCHHHHHHhhhhhh
Q 030808 46 DFPCPYCYE-DFDIASLCSHLEDEH 69 (171)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH 69 (171)
.|.|..|++ =-+...|..|....|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 377888888 556788888875544
No 46
>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=68.32 E-value=5.6 Score=31.96 Aligned_cols=34 Identities=21% Similarity=0.377 Sum_probs=25.5
Q ss_pred CCCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
.....|.||-|+.-++..+-.+ ..-.||+|-...
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEe
Confidence 4567899999999666555554 267999998875
No 47
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=68.05 E-value=3 Score=39.33 Aligned_cols=64 Identities=20% Similarity=0.384 Sum_probs=41.3
Q ss_pred CCCcCCCCCCCCCcccCCCCCC---CCCHHHHHHhhhhhhcCCCCccccCCcccc--------c---hhhHHhhhhhccc
Q 030808 33 SIDDFEVEDDVRPDFPCPYCYE---DFDIASLCSHLEDEHSCESKVTVCPICSVK--------V---ARDMLSHITLQHG 98 (171)
Q Consensus 33 g~e~~~~ddd~r~~F~CPfC~e---~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~--------~---s~d~l~HL~~qH~ 98 (171)
.+++.+.++.+++.|.||+|.. .||...|.. ++...-.|-.|-.- + +...++++.-|=.
T Consensus 115 rled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~-------~~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~~~~Q~~ 187 (436)
T KOG2593|consen 115 RLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLD-------NETGEFHCENCGGELVEDENKLPSKESRTALNRLMEQLE 187 (436)
T ss_pred HHHHHhhhccccccccCCccccchhhhHHHHhhc-------ccCceEEEecCCCchhcccccCchHHHHHHHHHHHHHHH
Confidence 3455555667899999999988 556666654 23445567777554 3 4455667766666
Q ss_pred chhhh
Q 030808 99 HLFKL 103 (171)
Q Consensus 99 ~~~k~ 103 (171)
..++.
T Consensus 188 pi~d~ 192 (436)
T KOG2593|consen 188 PIIDL 192 (436)
T ss_pred HHHHH
Confidence 66654
No 48
>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=67.64 E-value=3 Score=24.54 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=9.8
Q ss_pred CCCcccCCCCCC
Q 030808 43 VRPDFPCPYCYE 54 (171)
Q Consensus 43 ~r~~F~CPfC~e 54 (171)
.-..|.||-||+
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 356899999986
No 49
>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=67.44 E-value=1.5 Score=33.34 Aligned_cols=17 Identities=18% Similarity=0.704 Sum_probs=13.2
Q ss_pred CCCCCcccCCCCCC-CCC
Q 030808 41 DDVRPDFPCPYCYE-DFD 57 (171)
Q Consensus 41 dd~r~~F~CPfC~e-~fD 57 (171)
..+.+.|+||||+. .+.
T Consensus 30 ~~q~a~y~CpfCgk~~vk 47 (91)
T TIGR00280 30 IQQKAKYVCPFCGKKTVK 47 (91)
T ss_pred HHHhcCccCCCCCCCceE
Confidence 36788999999987 443
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=66.94 E-value=2.1 Score=26.47 Aligned_cols=26 Identities=27% Similarity=0.599 Sum_probs=16.5
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
.|.|+.||.-++... ..-+||||-+.
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 477888887333211 23489999874
No 51
>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=66.87 E-value=5.4 Score=37.90 Aligned_cols=41 Identities=32% Similarity=0.368 Sum_probs=32.2
Q ss_pred CCcccCCCCCC-CCCHHHHHHhhhhhhcCCCCc---cccCCcccc
Q 030808 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKV---TVCPICSVK 84 (171)
Q Consensus 44 r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~---vVCPVCaa~ 84 (171)
+.--.||+|.+ -.|..++..|+.++|...-.+ -+.|-....
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~ 99 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDD 99 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCH
Confidence 44678999999 999999999999999986543 355655443
No 52
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=66.77 E-value=2.5 Score=28.02 Aligned_cols=7 Identities=57% Similarity=1.829 Sum_probs=6.4
Q ss_pred cCCCCCC
Q 030808 48 PCPYCYE 54 (171)
Q Consensus 48 ~CPfC~e 54 (171)
+|||||.
T Consensus 3 PCPfCGg 9 (53)
T TIGR03655 3 PCPFCGG 9 (53)
T ss_pred CCCCCCC
Confidence 7999987
No 53
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=66.14 E-value=1.7 Score=32.94 Aligned_cols=17 Identities=24% Similarity=0.694 Sum_probs=13.1
Q ss_pred CCCCCcccCCCCCC-CCC
Q 030808 41 DDVRPDFPCPYCYE-DFD 57 (171)
Q Consensus 41 dd~r~~F~CPfC~e-~fD 57 (171)
..+.+.|+||||+. .+.
T Consensus 31 ~~q~a~y~CpfCgk~~vk 48 (90)
T PRK03976 31 EKMRAKHVCPVCGRPKVK 48 (90)
T ss_pred HHHhcCccCCCCCCCceE
Confidence 35678999999987 543
No 54
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.90 E-value=4.9 Score=33.05 Aligned_cols=34 Identities=24% Similarity=0.443 Sum_probs=24.4
Q ss_pred CCCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
.....|.||-|+.-|+..+-.+ ..-.||+|-...
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEML 146 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCC
Confidence 3457899999999555544322 357999998875
No 55
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=63.71 E-value=1.9 Score=28.28 Aligned_cols=45 Identities=36% Similarity=0.719 Sum_probs=28.0
Q ss_pred cccCCC--CCCCCCHHHHHHhhhhhhcCCCCccccCC----ccccc-hhhHHhh
Q 030808 46 DFPCPY--CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVKV-ARDMLSH 92 (171)
Q Consensus 46 ~F~CPf--C~e~fD~~~L~~H~~eeH~~e~k~vVCPV----Caa~~-s~d~l~H 92 (171)
...||+ |.+.+-...|-.|+..+=+ -+.+.||. |..++ ..++..|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~--~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECP--KRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTST--TSEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCC--CCcEECCCCCCCCCCccchhHHhCC
Confidence 568999 6667888888888885333 35789999 98876 4455544
No 56
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=63.48 E-value=3.1 Score=42.12 Aligned_cols=40 Identities=28% Similarity=0.544 Sum_probs=35.0
Q ss_pred CcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
+..+||||.. .-....|.+|+.-.|--..-+.-|+.|...
T Consensus 209 qlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsyt 249 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYT 249 (1007)
T ss_pred hhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhh
Confidence 4689999999 556789999999999987778889999876
No 57
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=63.25 E-value=5.7 Score=27.12 Aligned_cols=23 Identities=13% Similarity=0.353 Sum_probs=12.7
Q ss_pred CCCCCHHHHHHhhhhhhcCCCCccccCC
Q 030808 53 YEDFDIASLCSHLEDEHSCESKVTVCPI 80 (171)
Q Consensus 53 ~e~fD~~~L~~H~~eeH~~e~k~vVCPV 80 (171)
+--|+...+..++ ...+.+.||+
T Consensus 31 ~H~fek~aI~~~i-----~~~~~~~CPv 53 (57)
T PF11789_consen 31 GHTFEKEAILQYI-----QRNGSKRCPV 53 (57)
T ss_dssp --EEEHHHHHHHC-----TTTS-EE-SC
T ss_pred CCeecHHHHHHHH-----HhcCCCCCCC
Confidence 3346666666666 3456788998
No 58
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=59.82 E-value=4.2 Score=31.68 Aligned_cols=37 Identities=19% Similarity=0.456 Sum_probs=21.6
Q ss_pred CCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 43 ~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
+..+|+||+|+..--.+-+ -.-...-.+++|-+|-..
T Consensus 19 L~k~FtCp~Cghe~vs~ct-----vkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCT-----VKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred CCceEecCccCCeeeeEEE-----EEecCceeEEEcccCcce
Confidence 3468999999883322222 111122335889999764
No 59
>PF13395 HNH_4: HNH endonuclease
Probab=59.74 E-value=5.1 Score=26.58 Aligned_cols=14 Identities=43% Similarity=1.058 Sum_probs=12.2
Q ss_pred CCCCCCCCCHHHHH
Q 030808 49 CPYCYEDFDIASLC 62 (171)
Q Consensus 49 CPfC~e~fD~~~L~ 62 (171)
|||||+.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999988864
No 60
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=59.65 E-value=7 Score=27.60 Aligned_cols=33 Identities=30% Similarity=0.651 Sum_probs=22.6
Q ss_pred CCCcccCCCCCCC-CCHHHHHHhhhhhhcCCCCccccCCcc
Q 030808 43 VRPDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICS 82 (171)
Q Consensus 43 ~r~~F~CPfC~e~-fD~~~L~~H~~eeH~~e~k~vVCPVCa 82 (171)
.-..|.||-||+. +-. |..|.. .+..-+||-|-
T Consensus 22 ~~~~F~CPnCG~~~I~R---C~~CRk----~~~~Y~CP~CG 55 (59)
T PRK14890 22 KAVKFLCPNCGEVIIYR---CEKCRK----QSNPYTCPKCG 55 (59)
T ss_pred ccCEeeCCCCCCeeEee---chhHHh----cCCceECCCCC
Confidence 3568999999994 554 444443 25677899884
No 61
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.90 E-value=10 Score=32.25 Aligned_cols=44 Identities=20% Similarity=0.579 Sum_probs=27.1
Q ss_pred CCcccCCCCCCCCCHHH----HHHhhhhhhcC---CCCccccCCccccchh
Q 030808 44 RPDFPCPYCYEDFDIAS----LCSHLEDEHSC---ESKVTVCPICSVKVAR 87 (171)
Q Consensus 44 r~~F~CPfC~e~fD~~~----L~~H~~eeH~~---e~k~vVCPVCaa~~s~ 87 (171)
...|.||.|-+.+.... =|-|+-=.-+. =.+.++||+|..+++.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 35799999977555444 23443322222 1345789999988754
No 62
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=58.44 E-value=5.1 Score=26.25 Aligned_cols=28 Identities=21% Similarity=0.553 Sum_probs=21.0
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
.|.|.-||.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 57889998877754 34568899998765
No 63
>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=58.02 E-value=5.4 Score=32.38 Aligned_cols=54 Identities=26% Similarity=0.566 Sum_probs=31.1
Q ss_pred CcccCCC----CCCCCCHHHHHHhhhhhhcCCCCccccCC----cccc-chhhHHhhhhhcccchh
Q 030808 45 PDFPCPY----CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVK-VARDMLSHITLQHGHLF 101 (171)
Q Consensus 45 ~~F~CPf----C~e~fD~~~L~~H~~eeH~~e~k~vVCPV----Caa~-~s~d~l~HL~~qH~~~~ 101 (171)
-.|+||| |.+.+-......|.++ - .-++..||+ |.-. ...++..|+...|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~~-C--~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEEE-C--PFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHHT----TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhcc-C--CCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 4799999 8887777777776532 1 235678999 7433 46799999999998743
No 64
>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=57.04 E-value=11 Score=26.30 Aligned_cols=36 Identities=19% Similarity=0.381 Sum_probs=22.9
Q ss_pred CcccCCCCCC------------CCCHHHHHHhhhhhhcCCCCccccCCccccch
Q 030808 45 PDFPCPYCYE------------DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (171)
Q Consensus 45 ~~F~CPfC~e------------~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s 86 (171)
..|.||.|++ -||...+..++.. ...+||+|...++
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 4688888754 4677777777766 6678999966653
No 65
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.90 E-value=9.4 Score=31.40 Aligned_cols=47 Identities=19% Similarity=0.359 Sum_probs=32.5
Q ss_pred CCCcCCCCCCCCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccchhhHHhhhhh
Q 030808 33 SIDDFEVEDDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITL 95 (171)
Q Consensus 33 g~e~~~~ddd~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s~d~l~HL~~ 95 (171)
|+..+..+++..++=.||.||. ...+...||.|-...-+|..+=+++
T Consensus 296 ~~~~v~~~~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~Ni 342 (364)
T COG0675 296 GGIVVKVVPPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALNI 342 (364)
T ss_pred CCeEEEECCCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHHHH
Confidence 4444444445566688999998 3367789999998877776654433
No 66
>PRK12495 hypothetical protein; Provisional
Probab=56.64 E-value=6.7 Score=34.20 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=21.9
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
..|.||.||..+- .. ...++||+|-..+
T Consensus 41 sa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 41 TNAHCDECGDPIF------------RH-DGQEFCPTCQQPV 68 (226)
T ss_pred chhhcccccCccc------------CC-CCeeECCCCCCcc
Confidence 4689999999554 22 5678999999886
No 67
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=56.54 E-value=10 Score=34.02 Aligned_cols=59 Identities=24% Similarity=0.423 Sum_probs=39.7
Q ss_pred CCCcccCCCCCC-CCCHHHHHHhhhhhhcCC-CCccccCCcccc-chh-hHHhhhhhcccchhh
Q 030808 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCE-SKVTVCPICSVK-VAR-DMLSHITLQHGHLFK 102 (171)
Q Consensus 43 ~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e-~k~vVCPVCaa~-~s~-d~l~HL~~qH~~~~k 102 (171)
....|.||-|++ -=+...|-.|-+..=..+ .+.-.|++|-.. |+. -+-.||+. |.-..+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirT-H~l~c~ 189 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRT-HTLPCE 189 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhc-cCCCcc
Confidence 356899999999 667778999987654444 455779999654 443 35556643 443333
No 68
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.06 E-value=11 Score=26.88 Aligned_cols=34 Identities=29% Similarity=0.742 Sum_probs=21.2
Q ss_pred CCCCcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCcc
Q 030808 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICS 82 (171)
Q Consensus 42 d~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCa 82 (171)
+.-..|+||-||| .+-.-.-|.- -.+.-+||-|-
T Consensus 23 e~~v~F~CPnCGe~~I~Rc~~CRk-------~g~~Y~Cp~CG 57 (61)
T COG2888 23 ETAVKFPCPNCGEVEIYRCAKCRK-------LGNPYRCPKCG 57 (61)
T ss_pred CceeEeeCCCCCceeeehhhhHHH-------cCCceECCCcC
Confidence 3456899999997 5544333321 24456788774
No 69
>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=54.47 E-value=3.2 Score=26.50 Aligned_cols=31 Identities=23% Similarity=0.635 Sum_probs=21.2
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa 83 (171)
.+|.|+-||..|++..- ..+...+.||.|..
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 46899999976664311 12356789999977
No 70
>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=54.31 E-value=12 Score=25.24 Aligned_cols=48 Identities=25% Similarity=0.536 Sum_probs=32.7
Q ss_pred cCCCcCCCCCCCCCcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccccchhhHHhh
Q 030808 32 LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSH 92 (171)
Q Consensus 32 ~g~e~~~~ddd~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s~d~l~H 92 (171)
.|+.-+++++ .-.+=+||.||. .-+ ....+..+||.|-....+|+.+=
T Consensus 15 ~G~~v~~v~~-~~TSq~C~~CG~~~~~------------~~~~r~~~C~~Cg~~~~rD~naA 63 (69)
T PF07282_consen 15 YGIQVVEVDE-AYTSQTCPRCGHRNKK------------RRSGRVFTCPNCGFEMDRDVNAA 63 (69)
T ss_pred hCCEEEEECC-CCCccCccCccccccc------------ccccceEEcCCCCCEECcHHHHH
Confidence 3544444543 336788999998 333 55567789999988887776653
No 71
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=54.13 E-value=11 Score=23.64 Aligned_cols=20 Identities=30% Similarity=0.753 Sum_probs=12.1
Q ss_pred HHHhhhhhhcCCCCccccCCcc
Q 030808 61 LCSHLEDEHSCESKVTVCPICS 82 (171)
Q Consensus 61 L~~H~~eeH~~e~k~vVCPVCa 82 (171)
+|.-|..... .+.++||+|.
T Consensus 24 ~C~~C~~~~~--~~~~~CP~C~ 43 (44)
T PF14634_consen 24 FCEKCLKKLK--GKSVKCPICR 43 (44)
T ss_pred HHHHHHHhhc--CCCCCCcCCC
Confidence 3444444444 6678899885
No 72
>PF15616 TerY-C: TerY-C metal binding domain
Probab=52.65 E-value=3.4 Score=33.08 Aligned_cols=40 Identities=20% Similarity=0.432 Sum_probs=28.6
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcC-CCCccccCCccccchhh
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSC-ESKVTVCPICSVKVARD 88 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~-e~k~vVCPVCaa~~s~d 88 (171)
=.||+||..+-.+- | =|-.-|+. +...++||-|-....-.
T Consensus 78 PgCP~CGn~~~fa~-C-~CGkl~Ci~g~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 78 PGCPHCGNQYAFAV-C-GCGKLFCIDGEGEVTCPWCGNEGSFG 118 (131)
T ss_pred CCCCCCcChhcEEE-e-cCCCEEEeCCCCCEECCCCCCeeeec
Confidence 57999998544432 2 48888884 56679999998876433
No 73
>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=51.80 E-value=9.3 Score=22.54 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=3.7
Q ss_pred CCCCCCCC
Q 030808 49 CPYCYEDF 56 (171)
Q Consensus 49 CPfC~e~f 56 (171)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 45554433
No 74
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=50.97 E-value=7 Score=30.12 Aligned_cols=9 Identities=67% Similarity=1.575 Sum_probs=7.5
Q ss_pred cccCCCCCC
Q 030808 46 DFPCPYCYE 54 (171)
Q Consensus 46 ~F~CPfC~e 54 (171)
-++|||||+
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 468999998
No 75
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=49.04 E-value=12 Score=35.17 Aligned_cols=35 Identities=31% Similarity=0.747 Sum_probs=21.8
Q ss_pred CCCCCCCCCHHH-----------HHHhhhhhhcCCCCccccCCcccc
Q 030808 49 CPYCYEDFDIAS-----------LCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 49 CPfC~e~fD~~~-----------L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
||.|-|.+|+.+ .|..|- .|.-+.-++.||.|.-+
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~-~~irq~lngrcpacrr~ 62 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCY-NNIRQNLNGRCPACRRK 62 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHH-HHHHhhccCCChHhhhh
Confidence 777777666643 333332 23334478999999876
No 76
>PRK00420 hypothetical protein; Validated
Probab=48.58 E-value=13 Score=28.96 Aligned_cols=27 Identities=22% Similarity=0.405 Sum_probs=18.9
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
-.||.||-.|- ......++||+|...+
T Consensus 24 ~~CP~Cg~pLf------------~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLF------------ELKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcce------------ecCCCceECCCCCCee
Confidence 58999987432 1125578999998864
No 77
>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=48.34 E-value=17 Score=20.73 Aligned_cols=22 Identities=36% Similarity=0.715 Sum_probs=16.4
Q ss_pred HHHHhhhhhhcCCCCccccCCccc
Q 030808 60 SLCSHLEDEHSCESKVTVCPICSV 83 (171)
Q Consensus 60 ~L~~H~~eeH~~e~k~vVCPVCaa 83 (171)
.|..|+.. |..+ ++-.||+|..
T Consensus 1 ~l~~H~~~-H~~~-k~~~C~~C~k 22 (26)
T PF13465_consen 1 NLRRHMRT-HTGE-KPYKCPYCGK 22 (26)
T ss_dssp HHHHHHHH-HSSS-SSEEESSSSE
T ss_pred CHHHHhhh-cCCC-CCCCCCCCcC
Confidence 47788884 7765 6689999964
No 78
>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=48.31 E-value=7.3 Score=29.50 Aligned_cols=13 Identities=23% Similarity=0.986 Sum_probs=10.1
Q ss_pred CCCCcccCCCCCC
Q 030808 42 DVRPDFPCPYCYE 54 (171)
Q Consensus 42 d~r~~F~CPfC~e 54 (171)
.+...|.||||+.
T Consensus 31 ~q~~ky~Cp~Cgk 43 (90)
T PF01780_consen 31 SQHAKYTCPFCGK 43 (90)
T ss_dssp HHHS-BEESSSSS
T ss_pred HHhCCCcCCCCCC
Confidence 4567899999997
No 79
>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=47.10 E-value=10 Score=25.58 Aligned_cols=13 Identities=38% Similarity=0.945 Sum_probs=11.2
Q ss_pred CCCCcccCCCCCC
Q 030808 42 DVRPDFPCPYCYE 54 (171)
Q Consensus 42 d~r~~F~CPfC~e 54 (171)
++..+|.||.|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (50)
T cd00730 30 DLPDDWVCPVCGA 42 (50)
T ss_pred HCCCCCCCCCCCC
Confidence 5678999999987
No 80
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=46.94 E-value=13 Score=25.79 Aligned_cols=25 Identities=32% Similarity=0.861 Sum_probs=17.6
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
-.||.|++.|. .+.-.||||.|.+.
T Consensus 6 ~~C~~Cg~~~~-------------~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFK-------------DGDDIVVCPECGAP 30 (54)
T ss_pred ccChhhCCccc-------------CCCCEEECCCCCCc
Confidence 47888888662 12346899999875
No 81
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=46.81 E-value=16 Score=32.13 Aligned_cols=35 Identities=26% Similarity=0.425 Sum_probs=19.4
Q ss_pred CCCCcccCCCCCCCCCHHHHHHhhhhhhcCCC--CccccCCccccc
Q 030808 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCES--KVTVCPICSVKV 85 (171)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~--k~vVCPVCaa~~ 85 (171)
-.+...-||-|.- |-.-.|..|. ..-|||-|-+..
T Consensus 188 ~~~~alIC~~C~h---------hngl~~~~ek~~~efiC~~Cn~~n 224 (251)
T COG5415 188 SPFKALICPQCHH---------HNGLYRLAEKPIIEFICPHCNHKN 224 (251)
T ss_pred Cchhhhccccccc---------cccccccccccchheecccchhhc
Confidence 3456677888843 1112233221 246899997764
No 82
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=46.38 E-value=17 Score=22.59 Aligned_cols=31 Identities=26% Similarity=0.744 Sum_probs=18.4
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccc
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa 83 (171)
..||-|+..|++.+ +.=+...+.|.||-|..
T Consensus 3 i~CP~C~~~f~v~~------~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPD------DKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCH------HHcccCCcEEECCCCCc
Confidence 57888888444432 11123456788888864
No 83
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=45.63 E-value=12 Score=32.80 Aligned_cols=38 Identities=21% Similarity=0.549 Sum_probs=27.4
Q ss_pred CcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccccchhhHHhhh
Q 030808 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (171)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s~d~l~HL 93 (171)
....||.|+. ++ +.+ .+...+||.-|-..+..+++.+-
T Consensus 10 ~~~~Cp~Cg~~~i--------v~d---~~~Ge~vC~~CG~Vl~e~~iD~g 48 (310)
T PRK00423 10 EKLVCPECGSDKL--------IYD---YERGEIVCADCGLVIEENIIDQG 48 (310)
T ss_pred cCCcCcCCCCCCe--------eEE---CCCCeEeecccCCcccccccccC
Confidence 3457999996 22 112 35778999999999988877543
No 84
>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=45.38 E-value=6.4 Score=30.11 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=22.1
Q ss_pred CCCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
+.+..+.|+-|+..+..... ...||-|.+.
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 34668999999987666533 4679999864
No 85
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=45.27 E-value=14 Score=20.89 Aligned_cols=21 Identities=24% Similarity=0.393 Sum_probs=14.6
Q ss_pred ccCCCCCC-CCCHHHHHHhhhh
Q 030808 47 FPCPYCYE-DFDIASLCSHLED 67 (171)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~e 67 (171)
|.|+.|+. =-+...|..|+..
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 67888888 4566777777653
No 86
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=45.26 E-value=14 Score=28.81 Aligned_cols=29 Identities=21% Similarity=0.363 Sum_probs=22.9
Q ss_pred ccccCCccccc-----hhhHHhhhhhcccchhhh
Q 030808 75 VTVCPICSVKV-----ARDMLSHITLQHGHLFKL 103 (171)
Q Consensus 75 ~vVCPVCaa~~-----s~d~l~HL~~qH~~~~k~ 103 (171)
.+.||+|.... ...+..||+.-||-+-+.
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s~g 58 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISSTG 58 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhccccccCC
Confidence 78899998542 667999999999988743
No 87
>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=45.02 E-value=18 Score=21.06 Aligned_cols=23 Identities=30% Similarity=0.597 Sum_probs=16.4
Q ss_pred cccCCCCCCCCC-HHHHHHhhhhh
Q 030808 46 DFPCPYCYEDFD-IASLCSHLEDE 68 (171)
Q Consensus 46 ~F~CPfC~e~fD-~~~L~~H~~ee 68 (171)
.|.|.+|+..|+ ...+..|+...
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 477888888555 77777777643
No 88
>PRK03922 hypothetical protein; Provisional
Probab=44.60 E-value=11 Score=29.75 Aligned_cols=14 Identities=50% Similarity=0.736 Sum_probs=11.4
Q ss_pred cccCCCCCCCCCHH
Q 030808 46 DFPCPYCYEDFDIA 59 (171)
Q Consensus 46 ~F~CPfC~e~fD~~ 59 (171)
.-.||+||++||-.
T Consensus 49 ~~~cP~cge~~~~a 62 (113)
T PRK03922 49 LTICPKCGEPFDSA 62 (113)
T ss_pred cccCCCCCCcCCcE
Confidence 57899999998743
No 89
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=44.47 E-value=15 Score=21.19 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=5.7
Q ss_pred cCCCCCCCC
Q 030808 48 PCPYCYEDF 56 (171)
Q Consensus 48 ~CPfC~e~f 56 (171)
.||.||..+
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 577777643
No 90
>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=44.06 E-value=3 Score=25.33 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=5.2
Q ss_pred CCccccCCc
Q 030808 73 SKVTVCPIC 81 (171)
Q Consensus 73 ~k~vVCPVC 81 (171)
...+.||+|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 445556665
No 91
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=43.91 E-value=11 Score=29.20 Aligned_cols=14 Identities=50% Similarity=0.904 Sum_probs=11.4
Q ss_pred cccCCCCCCCCCHH
Q 030808 46 DFPCPYCYEDFDIA 59 (171)
Q Consensus 46 ~F~CPfC~e~fD~~ 59 (171)
.-.||+|+++|+-.
T Consensus 47 ~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 47 DTICPKCGEELDSA 60 (102)
T ss_pred cccCCCCCCccCce
Confidence 57899999988743
No 92
>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=43.09 E-value=9.5 Score=25.16 Aligned_cols=14 Identities=29% Similarity=0.591 Sum_probs=7.9
Q ss_pred cCCCCCCCCCHHHH
Q 030808 48 PCPYCYEDFDIASL 61 (171)
Q Consensus 48 ~CPfC~e~fD~~~L 61 (171)
.||.|+.+||...-
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 89999998887654
No 93
>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=42.72 E-value=13 Score=23.15 Aligned_cols=25 Identities=28% Similarity=0.590 Sum_probs=10.8
Q ss_pred CcccCCCCCCCCCH-----HHHHHhhhhhh
Q 030808 45 PDFPCPYCYEDFDI-----ASLCSHLEDEH 69 (171)
Q Consensus 45 ~~F~CPfC~e~fD~-----~~L~~H~~eeH 69 (171)
....|-||+..+.. ..|..|+...|
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 34556666553333 35555554444
No 94
>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=42.06 E-value=3 Score=34.20 Aligned_cols=39 Identities=26% Similarity=0.636 Sum_probs=19.4
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
-.|.||.|+..+...++.. .+.-........||-|....
T Consensus 17 l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 17 LKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B-
T ss_pred eEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcC
Confidence 4799999999666666444 11122234567899998864
No 95
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=41.79 E-value=7.8 Score=29.50 Aligned_cols=15 Identities=13% Similarity=0.707 Sum_probs=12.3
Q ss_pred CCCCcccCCCCCC-CC
Q 030808 42 DVRPDFPCPYCYE-DF 56 (171)
Q Consensus 42 d~r~~F~CPfC~e-~f 56 (171)
-+.+.|.|+|||+ .+
T Consensus 32 ~Qhaky~CsfCGK~~v 47 (92)
T KOG0402|consen 32 QQHAKYTCSFCGKKTV 47 (92)
T ss_pred HHhhhhhhhhcchhhh
Confidence 5678999999998 44
No 96
>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=41.51 E-value=16 Score=30.78 Aligned_cols=36 Identities=31% Similarity=0.572 Sum_probs=22.4
Q ss_pred CCCCCC--CCCHHHHHHhhhhhhcC------CCCccccCCcccc
Q 030808 49 CPYCYE--DFDIASLCSHLEDEHSC------ESKVTVCPICSVK 84 (171)
Q Consensus 49 CPfC~e--~fD~~~L~~H~~eeH~~------e~k~vVCPVCaa~ 84 (171)
||.||. +-...+||.=|-.+... .-...+||.|-+.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~ 44 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRY 44 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCE
Confidence 777876 33345677666554432 2245789999775
No 97
>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=40.54 E-value=13 Score=24.68 Aligned_cols=13 Identities=38% Similarity=0.945 Sum_probs=8.2
Q ss_pred CCCCcccCCCCCC
Q 030808 42 DVRPDFPCPYCYE 54 (171)
Q Consensus 42 d~r~~F~CPfC~e 54 (171)
++...|.||-|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 30 DLPDDWVCPVCGA 42 (47)
T ss_dssp GS-TT-B-TTTSS
T ss_pred HCCCCCcCcCCCC
Confidence 5677899999986
No 98
>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=40.37 E-value=21 Score=22.26 Aligned_cols=20 Identities=30% Similarity=0.615 Sum_probs=13.6
Q ss_pred CccccCCccccc-hhhHHhhh
Q 030808 74 KVTVCPICSVKV-ARDMLSHI 93 (171)
Q Consensus 74 k~vVCPVCaa~~-s~d~l~HL 93 (171)
..+.||.|.-.+ ..-|..||
T Consensus 3 ~~~~C~nC~R~v~a~RfA~HL 23 (33)
T PF08209_consen 3 PYVECPNCGRPVAASRFAPHL 23 (33)
T ss_dssp -EEE-TTTSSEEEGGGHHHHH
T ss_pred CeEECCCCcCCcchhhhHHHH
Confidence 357899997776 55688887
No 99
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=40.18 E-value=6 Score=30.05 Aligned_cols=16 Identities=31% Similarity=0.864 Sum_probs=12.9
Q ss_pred CCCCCCCcccCCCCCC
Q 030808 39 VEDDVRPDFPCPYCYE 54 (171)
Q Consensus 39 ~ddd~r~~F~CPfC~e 54 (171)
.|..+++.+.||+|+.
T Consensus 28 ie~~~~~~~~Cp~C~~ 43 (89)
T COG1997 28 IEAQQRAKHVCPFCGR 43 (89)
T ss_pred HHHHHhcCCcCCCCCC
Confidence 3446788999999987
No 100
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=39.79 E-value=16 Score=25.33 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=10.4
Q ss_pred CCCCcccCCCCCC
Q 030808 42 DVRPDFPCPYCYE 54 (171)
Q Consensus 42 d~r~~F~CPfC~e 54 (171)
..+..|+||.||-
T Consensus 10 ~~~v~~~Cp~cGi 22 (55)
T PF13824_consen 10 PAHVNFECPDCGI 22 (55)
T ss_pred ccccCCcCCCCCC
Confidence 4467899999975
No 101
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=39.64 E-value=16 Score=30.32 Aligned_cols=25 Identities=36% Similarity=0.822 Sum_probs=18.1
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
.+.||.||-- |.. -.+.+||||-+.
T Consensus 134 ~~vC~vCGy~-------------~~g-e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYT-------------HEG-EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCc-------------ccC-CCCCcCCCCCCh
Confidence 8999999641 122 346899999865
No 102
>PRK12496 hypothetical protein; Provisional
Probab=39.52 E-value=21 Score=28.93 Aligned_cols=28 Identities=25% Similarity=0.481 Sum_probs=20.0
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccch
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s 86 (171)
.|.||-|++.|+.. ...-+||||-+.+.
T Consensus 127 ~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPED-------------YPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCC-------------CCCCcCCCCCChhh
Confidence 48899999877631 22358999987653
No 103
>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=39.42 E-value=16 Score=24.89 Aligned_cols=10 Identities=40% Similarity=1.228 Sum_probs=8.4
Q ss_pred CcccCCCCCC
Q 030808 45 PDFPCPYCYE 54 (171)
Q Consensus 45 ~~F~CPfC~e 54 (171)
-+|.||+|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 3899999986
No 104
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=39.41 E-value=6.2 Score=33.23 Aligned_cols=26 Identities=15% Similarity=0.470 Sum_probs=15.2
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcC
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSC 71 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~ 71 (171)
.|.||.|+..+.+.+=-=+|...|.+
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCC
Confidence 48999999866432211234445555
No 105
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.34 E-value=14 Score=32.39 Aligned_cols=44 Identities=27% Similarity=0.612 Sum_probs=30.7
Q ss_pred CCcccCCCCCC--CCCHHHHHHhhh-------hhhcCCCCccccCCccccchhh
Q 030808 44 RPDFPCPYCYE--DFDIASLCSHLE-------DEHSCESKVTVCPICSVKVARD 88 (171)
Q Consensus 44 r~~F~CPfC~e--~fD~~~L~~H~~-------eeH~~e~k~vVCPVCaa~~s~d 88 (171)
-..|.|-.|.+ .==|..||-|+- --|. ......||||-+.|+.+
T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~-~~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQT-RPNSKECPVCKAEVSID 97 (230)
T ss_pred CCceeeeeeccccCCCEEeecccceehHHHHHHHhh-cCCCeeCCccccccccc
Confidence 35799999987 555788988862 2222 23456899999987544
No 106
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.39 E-value=13 Score=28.77 Aligned_cols=37 Identities=24% Similarity=0.620 Sum_probs=22.9
Q ss_pred CcccCCCCCCCCCHH-------HHHHhhhhhhcCCCCccccCCccc
Q 030808 45 PDFPCPYCYEDFDIA-------SLCSHLEDEHSCESKVTVCPICSV 83 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~-------~L~~H~~eeH~~e~k~vVCPVCaa 83 (171)
..+.||.|-+.|... .+|.-|...... ....||+|..
T Consensus 12 ~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~--~~~~Cp~cr~ 55 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLPCGHNFCRACLTRSWE--GPLSCPVCRP 55 (386)
T ss_pred ccccChhhHHHhhcCccccccchHhHHHHHHhcC--CCcCCcccCC
Confidence 478999998755544 223333333333 4489999993
No 107
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=37.97 E-value=38 Score=32.03 Aligned_cols=49 Identities=27% Similarity=0.521 Sum_probs=36.5
Q ss_pred CcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccccc--hhhHHhhhh
Q 030808 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHIT 94 (171)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~--s~d~l~HL~ 94 (171)
..|+||.|+- ==..++|-.|+.-.|.- .+.-.|--|...- -.|+..|+.
T Consensus 262 n~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 262 NCYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred hcccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhhhccHHHHHHHHH
Confidence 4688999988 34567888999988877 7778888887762 446666665
No 108
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=37.92 E-value=19 Score=23.35 Aligned_cols=26 Identities=27% Similarity=0.589 Sum_probs=15.5
Q ss_pred CcccCCCCCCCCCH------HHHHHhhhhhhc
Q 030808 45 PDFPCPYCYEDFDI------ASLCSHLEDEHS 70 (171)
Q Consensus 45 ~~F~CPfC~e~fD~------~~L~~H~~eeH~ 70 (171)
+.-.|-+|+..+.. ..|..|+...|+
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 45667777764443 356666665554
No 109
>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=37.00 E-value=26 Score=31.76 Aligned_cols=39 Identities=26% Similarity=0.495 Sum_probs=25.0
Q ss_pred cccCCCCCC--CCCHH----------HHHHhhhhhhcCCCCccccCCccccc
Q 030808 46 DFPCPYCYE--DFDIA----------SLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 46 ~F~CPfC~e--~fD~~----------~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
.+.||.|.. -++-. .+|..|.+..-. .....||+|-..+
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~-~~~~~CP~C~~~l 53 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV-RGSGSCPECDTPL 53 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc-CCCCCCCCCCCcc
Confidence 368999966 22221 356777777643 3456999997654
No 110
>smart00507 HNHc HNH nucleases.
Probab=36.77 E-value=4.7 Score=24.35 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=13.2
Q ss_pred ccCCCCCCCCCHHHHHHhhhh
Q 030808 47 FPCPYCYEDFDIASLCSHLED 67 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~e 67 (171)
+.|+||++.++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 789999996553233444443
No 111
>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=36.67 E-value=20 Score=22.99 Aligned_cols=11 Identities=36% Similarity=0.857 Sum_probs=8.5
Q ss_pred CCcccCCCCCC
Q 030808 44 RPDFPCPYCYE 54 (171)
Q Consensus 44 r~~F~CPfC~e 54 (171)
...|.||.||-
T Consensus 16 ~~g~~CP~Cg~ 26 (46)
T PF12760_consen 16 PDGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCCC
Confidence 34689999985
No 112
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=36.56 E-value=16 Score=33.84 Aligned_cols=58 Identities=29% Similarity=0.559 Sum_probs=34.9
Q ss_pred cccCCCCCCCCCHHH---HHHhhhhhhcCCCC-ccccCCccccc--------------------------hhhHHhhhhh
Q 030808 46 DFPCPYCYEDFDIAS---LCSHLEDEHSCESK-VTVCPICSVKV--------------------------ARDMLSHITL 95 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~---L~~H~~eeH~~e~k-~vVCPVCaa~~--------------------------s~d~l~HL~~ 95 (171)
.-.|--|+.-+-+-+ =|+|+-=.-+.-+. -.+||.|..+| -+||-.||++
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~VqrIeq~~~g~iFmC~~~~GC~RTyLsqrDlqAHInh 169 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQRIEQIMMGGIFMCAAPHGCLRTYLSQRDLQAHINH 169 (389)
T ss_pred eEeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHHHHHhcccceEEeecchhHHHHHhhHHHHHHHhhh
Confidence 445555555333332 24443322222111 46899999874 4799999999
Q ss_pred cccchhhh
Q 030808 96 QHGHLFKL 103 (171)
Q Consensus 96 qH~~~~k~ 103 (171)
+|+...+-
T Consensus 170 rH~~~~~p 177 (389)
T KOG2932|consen 170 RHGSLLQP 177 (389)
T ss_pred hhccccCC
Confidence 99976644
No 113
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=36.49 E-value=10 Score=33.94 Aligned_cols=18 Identities=22% Similarity=0.458 Sum_probs=8.5
Q ss_pred CCCcccCCCCCC--CCCHHH
Q 030808 43 VRPDFPCPYCYE--DFDIAS 60 (171)
Q Consensus 43 ~r~~F~CPfC~e--~fD~~~ 60 (171)
-..+-.|+||+. .||..+
T Consensus 263 g~iev~C~FC~~~Y~f~~~e 282 (286)
T COG1281 263 GGIEVTCEFCGTKYLFDEEE 282 (286)
T ss_pred CCeEEEeeccCCEEecCHHH
Confidence 344455555554 444443
No 114
>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=36.14 E-value=20 Score=27.54 Aligned_cols=28 Identities=29% Similarity=0.736 Sum_probs=15.2
Q ss_pred CcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
....||-||. =+|+. ..++|||-|.+..
T Consensus 8 tKR~Cp~CG~kFYDLn-------------k~PivCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLN-------------KDPIVCPKCGTEF 36 (108)
T ss_pred CcccCCCCcchhccCC-------------CCCccCCCCCCcc
Confidence 4456666666 33333 3456666665553
No 115
>PHA00733 hypothetical protein
Probab=36.11 E-value=35 Score=26.59 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=21.7
Q ss_pred cccCCCCCC-CCCHHHHHHhhhhhhc
Q 030808 46 DFPCPYCYE-DFDIASLCSHLEDEHS 70 (171)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~ 70 (171)
.|.|+.|++ --....|..|....|.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 599999999 4566889999999996
No 116
>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=35.89 E-value=1.2 Score=32.39 Aligned_cols=52 Identities=25% Similarity=0.431 Sum_probs=21.6
Q ss_pred cCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc-------hhhHHhhhhhcccchhhh
Q 030808 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV-------ARDMLSHITLQHGHLFKL 103 (171)
Q Consensus 48 ~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~-------s~d~l~HL~~qH~~~~k~ 103 (171)
.||-|..+++..+-.-||..=...=.+.+.||-|-..+ ..|+.= +|++..+.
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC----~~c~gLiS 61 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFC----NHCHGLIS 61 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceee----ccCCceee
Confidence 45556555555442222211111123457899998874 346654 46666654
No 117
>PRK11595 DNA utilization protein GntX; Provisional
Probab=35.75 E-value=19 Score=30.06 Aligned_cols=21 Identities=19% Similarity=0.325 Sum_probs=12.0
Q ss_pred cCCCCCCCCC--HHHHHHhhhhh
Q 030808 48 PCPYCYEDFD--IASLCSHLEDE 68 (171)
Q Consensus 48 ~CPfC~e~fD--~~~L~~H~~ee 68 (171)
.|+.|++.++ ...||..|.+.
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~ 29 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRA 29 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhh
Confidence 3777776432 23467777654
No 118
>PF14353 CpXC: CpXC protein
Probab=35.53 E-value=16 Score=27.58 Aligned_cols=29 Identities=28% Similarity=0.377 Sum_probs=18.5
Q ss_pred CCcccCCCCCCCCCHHHHHHhhhhhhcCCCCcc
Q 030808 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVT 76 (171)
Q Consensus 44 r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~v 76 (171)
-..|+||.||..+-+ .+--.+|-.+.+.+
T Consensus 36 l~~~~CP~Cg~~~~~----~~p~lY~D~~~~~~ 64 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRL----EYPLLYHDPEKKFM 64 (128)
T ss_pred cCEEECCCCCCceec----CCCEEEEcCCCCEE
Confidence 357999999995543 34445555555543
No 119
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=35.27 E-value=12 Score=28.54 Aligned_cols=30 Identities=20% Similarity=0.331 Sum_probs=20.9
Q ss_pred CCCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
..+..+.|+-|+..|.... ....||-|-..
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 3467899999997655433 33459999764
No 120
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=34.91 E-value=16 Score=30.63 Aligned_cols=17 Identities=24% Similarity=0.729 Sum_probs=13.6
Q ss_pred cccCCCCCCCCCHHHHH
Q 030808 46 DFPCPYCYEDFDIASLC 62 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~ 62 (171)
+++||+|+..|....+.
T Consensus 5 ~~~CPvC~~~F~~~~vr 21 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVR 21 (214)
T ss_pred ceECCCCCCeeeeeEEE
Confidence 68999999988876443
No 121
>PHA02929 N1R/p28-like protein; Provisional
Probab=34.87 E-value=19 Score=31.27 Aligned_cols=42 Identities=24% Similarity=0.501 Sum_probs=23.5
Q ss_pred CCcccCCCCCCCCCHH----------HHHHhhhhhhcC---CCCccccCCccccc
Q 030808 44 RPDFPCPYCYEDFDIA----------SLCSHLEDEHSC---ESKVTVCPICSVKV 85 (171)
Q Consensus 44 r~~F~CPfC~e~fD~~----------~L~~H~~eeH~~---e~k~vVCPVCaa~~ 85 (171)
.....||.|.+.+... .=|.|.--..+. -.....||+|...+
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~ 226 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF 226 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence 3467999998865322 114442221111 12355899998764
No 122
>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=34.56 E-value=28 Score=27.98 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=14.9
Q ss_pred CcccCCCCCC---CCCHHHHHHhh
Q 030808 45 PDFPCPYCYE---DFDIASLCSHL 65 (171)
Q Consensus 45 ~~F~CPfC~e---~fD~~~L~~H~ 65 (171)
..|.||-||. .+|-..+..=+
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i~~l 150 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAIEKL 150 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHHHHH
Confidence 4799999998 56655555433
No 123
>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=33.75 E-value=20 Score=34.14 Aligned_cols=47 Identities=34% Similarity=0.459 Sum_probs=33.4
Q ss_pred CCHHHHHHhhhhhhcCCC-----------------CccccCCccccc--hhhHHhhhhhcccchhh
Q 030808 56 FDIASLCSHLEDEHSCES-----------------KVTVCPICSVKV--ARDMLSHITLQHGHLFK 102 (171)
Q Consensus 56 fD~~~L~~H~~eeH~~e~-----------------k~vVCPVCaa~~--s~d~l~HL~~qH~~~~k 102 (171)
+++..|..|+...|..+. +.-+||+|..+- ...+..|+-..|-..++
T Consensus 21 Vsi~eL~sy~~~~~~~~a~~~Lseal~fak~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 21 VSIDELKSYYESVYDREAADALSEALSFAKENKSWRFWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eEHHHHHHHHHhccchHHHHHHHHHHHHHHhcCceeEeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 346677777776654322 235699999764 67899999999987763
No 124
>COG3326 Predicted membrane protein [Function unknown]
Probab=33.20 E-value=35 Score=26.12 Aligned_cols=30 Identities=33% Similarity=0.471 Sum_probs=17.8
Q ss_pred hcccccCCCCCchhHhhhhhhhhhhhhhHHhcCc-c-hhhhhhhh
Q 030808 106 RRRLRRVAIPSSQALSLLGRDLREAHLQVLLGVL-K-ILVQKVLH 148 (171)
Q Consensus 106 ~rr~rr~~~ps~s~ls~L~k~lre~~lq~llgg~-s-~~~~~~~~ 148 (171)
+++.+| +|+ ++| .+.+|+||+ + ...+.+.|
T Consensus 31 ~~~~wR--IpE-~~L----------l~~allGG~~Ga~~a~~~fr 62 (94)
T COG3326 31 RKGKWR--IPE-KTL----------LLIALLGGWFGAWLAMQLFR 62 (94)
T ss_pred HccCCC--CcH-HHH----------HHHHHHcchHHHHHHHHHHH
Confidence 444444 577 665 366899987 4 44444443
No 125
>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=33.07 E-value=18 Score=28.45 Aligned_cols=13 Identities=23% Similarity=0.777 Sum_probs=8.6
Q ss_pred CCCccccCCcccc
Q 030808 72 ESKVTVCPICSVK 84 (171)
Q Consensus 72 e~k~vVCPVCaa~ 84 (171)
+....|||-|+--
T Consensus 16 dg~~~iCpeC~~E 28 (109)
T TIGR00686 16 DGTQLICPSCLYE 28 (109)
T ss_pred cCCeeECcccccc
Confidence 3445788888654
No 126
>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=32.99 E-value=16 Score=28.97 Aligned_cols=41 Identities=20% Similarity=0.566 Sum_probs=29.0
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccchhhHH
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s~d~l 90 (171)
..+.|.-|+..++...+........ ...||.|...+..|++
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~-----~~~C~~C~~~lrp~vv 144 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEE-----PPRCPKCGGLLRPDVV 144 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTS-----SCBCTTTSCBEEEEE-
T ss_pred ceeeecCCCccccchhhcccccccc-----cccccccCccCCCCee
Confidence 3589999999888777765544332 2399999997766654
No 127
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.64 E-value=21 Score=25.52 Aligned_cols=13 Identities=38% Similarity=0.976 Sum_probs=7.2
Q ss_pred CCCccccCCcccc
Q 030808 72 ESKVTVCPICSVK 84 (171)
Q Consensus 72 e~k~vVCPVCaa~ 84 (171)
+.+.|+||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 4455666666543
No 128
>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=32.53 E-value=14 Score=25.09 Aligned_cols=45 Identities=24% Similarity=0.552 Sum_probs=29.5
Q ss_pred CCCcCCCCC-CCCCcccCCCCCC--CCCHHHHHHhhhhhhcCCCCccccCCccccch
Q 030808 33 SIDDFEVED-DVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (171)
Q Consensus 33 g~e~~~~dd-d~r~~F~CPfC~e--~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s 86 (171)
.+||++.++ +..-+|+| =||. .++...|-++ .-.|-|+-|+-.+.
T Consensus 4 ~l~d~~~~~~~~~~~y~C-RCG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 4 SLDDMEFDEEEGVYSYPC-RCGGEFEISEEDLEEG--------EVIVQCDSCSLWIR 51 (55)
T ss_dssp ETTTSEEETTTTEEEEEE-TTSSEEEEEHHHHHCT----------EEEETTTTEEEE
T ss_pred EhhhceecCCCCEEEEcC-CCCCEEEEcchhccCc--------CEEEECCCCccEEE
Confidence 345555433 33578999 6987 7777777666 44577999987653
No 129
>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=32.46 E-value=26 Score=24.12 Aligned_cols=39 Identities=23% Similarity=0.424 Sum_probs=24.4
Q ss_pred CcccCCCCCCCCCHHHHHHhh-----------------hhhhcCCCCccccCCccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHL-----------------EDEHSCESKVTVCPICSV 83 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~-----------------~eeH~~e~k~vVCPVCaa 83 (171)
....||+|.-.+|-..|+.=. .-+........+||-|..
T Consensus 6 niL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r 61 (68)
T PF03966_consen 6 NILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVEGELICPECGR 61 (68)
T ss_dssp GTBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTE
T ss_pred hhhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccCCEEEcCCCCC
Confidence 357899998888777776622 222233446789999953
No 130
>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=32.25 E-value=20 Score=26.76 Aligned_cols=8 Identities=63% Similarity=1.767 Sum_probs=5.2
Q ss_pred ccCCCCCC
Q 030808 47 FPCPYCYE 54 (171)
Q Consensus 47 F~CPfC~e 54 (171)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 36777774
No 131
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=32.24 E-value=23 Score=24.70 Aligned_cols=13 Identities=31% Similarity=0.874 Sum_probs=9.3
Q ss_pred cccCCCCCCCCCH
Q 030808 46 DFPCPYCYEDFDI 58 (171)
Q Consensus 46 ~F~CPfC~e~fD~ 58 (171)
.=.||||+.-||.
T Consensus 39 YngCPfC~~~~~~ 51 (55)
T PF14447_consen 39 YNGCPFCGTPFEF 51 (55)
T ss_pred ccCCCCCCCcccC
Confidence 3459999986653
No 132
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.14 E-value=9.2 Score=35.13 Aligned_cols=40 Identities=25% Similarity=0.571 Sum_probs=31.6
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcCCC---------CccccCCccccc
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSCES---------KVTVCPICSVKV 85 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~---------k~vVCPVCaa~~ 85 (171)
++.|-.|-|+|...+.+.++-=.|.+-. ..-.||||-..+
T Consensus 229 ~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 229 TDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred CceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 3999999999998888888877777622 246799998765
No 133
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.96 E-value=16 Score=28.70 Aligned_cols=43 Identities=16% Similarity=0.454 Sum_probs=23.6
Q ss_pred CCCCcccCCCCCCCCCHHHHHHhhh-----hhhcCC---CCccccCCcccc
Q 030808 42 DVRPDFPCPYCYEDFDIASLCSHLE-----DEHSCE---SKVTVCPICSVK 84 (171)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~-----eeH~~e---~k~vVCPVCaa~ 84 (171)
..+..+.|+-||..+...+--.++. .-|-.. .....||.|-+.
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 3467899999998555432111111 111111 244679999764
No 134
>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=31.76 E-value=8.2 Score=28.93 Aligned_cols=38 Identities=29% Similarity=0.679 Sum_probs=11.8
Q ss_pred cCCCCCCCCCHHHHH-HhhhhhhcC-----------CCCccccCCccccc
Q 030808 48 PCPYCYEDFDIASLC-SHLEDEHSC-----------ESKVTVCPICSVKV 85 (171)
Q Consensus 48 ~CPfC~e~fD~~~L~-~H~~eeH~~-----------e~k~vVCPVCaa~~ 85 (171)
.||+|++.++..++. .=|..-|.. +++.-+|++|..+.
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 599999977666543 347777765 45557788887654
No 135
>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=31.74 E-value=19 Score=27.28 Aligned_cols=19 Identities=21% Similarity=0.627 Sum_probs=12.9
Q ss_pred CcccCCCCCC-CCCHHHHHH
Q 030808 45 PDFPCPYCYE-DFDIASLCS 63 (171)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~ 63 (171)
..|.||+|.. +=.+..+..
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~~ 42 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWVK 42 (178)
T ss_pred ECCCCcchhhhhHHHHHHHH
Confidence 4699999988 544444444
No 136
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=31.56 E-value=26 Score=25.04 Aligned_cols=26 Identities=35% Similarity=0.828 Sum_probs=18.2
Q ss_pred cccCCccccc--hhhHHhhhhhcccchh
Q 030808 76 TVCPICSVKV--ARDMLSHITLQHGHLF 101 (171)
Q Consensus 76 vVCPVCaa~~--s~d~l~HL~~qH~~~~ 101 (171)
..||-|.+.- ..|.++|.+-.|+..+
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH~~~~ 45 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAHGWLF 45 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHhhhhh
Confidence 4566665542 6678888888888776
No 137
>PF08368 FAST_2: FAST kinase-like protein, subdomain 2; InterPro: IPR013579 This domain represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (2.7.1 from EC) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis []. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.
Probab=31.26 E-value=23 Score=25.77 Aligned_cols=28 Identities=29% Similarity=0.380 Sum_probs=21.7
Q ss_pred hhhhhhhhhhhhHHhcCcchhhhhhhhhh
Q 030808 122 LLGRDLREAHLQVLLGVLKILVQKVLHQH 150 (171)
Q Consensus 122 ~L~k~lre~~lq~llgg~s~~~~~~~~~~ 150 (171)
-+-++++++ |++||||..++-..|..++
T Consensus 48 ~~~~~v~~~-L~~lLg~~~~~~~~v~tp~ 75 (93)
T PF08368_consen 48 PLQQEVQEA-LKSLLGGENYFRSNVITPY 75 (93)
T ss_pred hHHHHHHHH-HHHHhCCccceEEccccCC
Confidence 366677776 9999999998877777665
No 138
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.03 E-value=27 Score=32.80 Aligned_cols=15 Identities=33% Similarity=0.811 Sum_probs=10.9
Q ss_pred CcccCCCCCCCCCHH
Q 030808 45 PDFPCPYCYEDFDIA 59 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~ 59 (171)
.+|.||||..+-+.+
T Consensus 373 ~sfKCPYCP~e~~~~ 387 (394)
T KOG2817|consen 373 QSFKCPYCPVEQLAS 387 (394)
T ss_pred eeeeCCCCCcccCHH
Confidence 369999998755443
No 139
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=30.90 E-value=18 Score=34.38 Aligned_cols=21 Identities=24% Similarity=0.561 Sum_probs=15.9
Q ss_pred hhhhhcCCCCccccCCccccc
Q 030808 65 LEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 65 ~~eeH~~e~k~vVCPVCaa~~ 85 (171)
|..+...+++.-|||||...|
T Consensus 27 c~~~~~~~PNt~vcpv~lg~P 47 (474)
T PRK05477 27 CSTDFGAEPNTNVCPVCLGLP 47 (474)
T ss_pred CCcccCCCCCCCcCccccCCC
Confidence 444445577889999999986
No 140
>PF14968 CCDC84: Coiled coil protein 84
Probab=30.83 E-value=25 Score=32.18 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=18.7
Q ss_pred CCCCCcccCCCCCCCCCHH-------HHHHhhh
Q 030808 41 DDVRPDFPCPYCYEDFDIA-------SLCSHLE 66 (171)
Q Consensus 41 dd~r~~F~CPfC~e~fD~~-------~L~~H~~ 66 (171)
.+.+..|=|+||+.++... ++..|+-
T Consensus 53 ~~~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLa 85 (336)
T PF14968_consen 53 PEHRNRFWCVFCDCEVREHDSSFACGGAIEHLA 85 (336)
T ss_pred ccccceeEeeCccchhhhccchhhhccHHhhcC
Confidence 3567899999999877654 5555543
No 141
>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=30.38 E-value=16 Score=34.28 Aligned_cols=34 Identities=35% Similarity=0.926 Sum_probs=15.5
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCc-cccchhhHHh
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPIC-SVKVARDMLS 91 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVC-aa~~s~d~l~ 91 (171)
+.-.||||+..+ |+ +-+--+|||| .+.++.+-++
T Consensus 379 ~~v~CP~cgA~y------------~~-~~kG~lC~vC~l~~IG~~a~G 413 (422)
T PF06957_consen 379 PSVKCPYCGAKY------------HP-EYKGQLCPVCELSEIGADASG 413 (422)
T ss_dssp -EEE-TTT--EE------------EG-GGTTSB-TTTTTBBTT---S-
T ss_pred CCeeCCCCCCcc------------Ch-hhCCCCCCCCcceeeCCccee
Confidence 446799998633 22 2345699999 4566665443
No 142
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=29.69 E-value=26 Score=32.73 Aligned_cols=40 Identities=23% Similarity=0.517 Sum_probs=31.5
Q ss_pred cccCCC--CCC-CCCHHHHHHhhhhhhcC-----------------CCCccccCCccccc
Q 030808 46 DFPCPY--CYE-DFDIASLCSHLEDEHSC-----------------ESKVTVCPICSVKV 85 (171)
Q Consensus 46 ~F~CPf--C~e-~fD~~~L~~H~~eeH~~-----------------e~k~vVCPVCaa~~ 85 (171)
-|.||. |.+ --++.+|.-|...-|+. +.|+-+|+||..+-
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 489987 877 77888999999888832 44677899998763
No 143
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.67 E-value=43 Score=20.77 Aligned_cols=31 Identities=19% Similarity=0.591 Sum_probs=17.1
Q ss_pred ccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccc
Q 030808 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa 83 (171)
+.||-|...|++.+- .=+.....|-||.|..
T Consensus 3 i~Cp~C~~~y~i~d~------~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDE------KIPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHH------HCCCCCcEEECCCCCC
Confidence 567888774444321 1133445677777754
No 144
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=28.97 E-value=32 Score=28.78 Aligned_cols=31 Identities=29% Similarity=0.611 Sum_probs=23.1
Q ss_pred CCCcccCCCCCC--CCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 43 VRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 43 ~r~~F~CPfC~e--~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
...-|.||-|.. .||.+-+.. -.||.|-+.+
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~~~------------F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAMELG------------FTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHHHHhC------------CCCCCCCchh
Confidence 456899999988 666554433 6899998875
No 145
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=28.94 E-value=41 Score=33.46 Aligned_cols=56 Identities=25% Similarity=0.557 Sum_probs=36.9
Q ss_pred CCCCCCCCcccCCCCCC-CCC-HHHHHHh-----hhh---hhcCCCCccccCCccccchhhHHhhh
Q 030808 38 EVEDDVRPDFPCPYCYE-DFD-IASLCSH-----LED---EHSCESKVTVCPICSVKVARDMLSHI 93 (171)
Q Consensus 38 ~~ddd~r~~F~CPfC~e-~fD-~~~L~~H-----~~e---eH~~e~k~vVCPVCaa~~s~d~l~HL 93 (171)
...||+...-.|-+|.+ .=| +.+-|-| |.. +-..+..+|.||+|.-..+-|+..|-
T Consensus 528 n~~~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 528 NLPDENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred CCCccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 34567888999999977 323 2333333 332 22347788999999998887766554
No 146
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=28.82 E-value=33 Score=31.52 Aligned_cols=41 Identities=29% Similarity=0.517 Sum_probs=31.0
Q ss_pred CCcccCCCCCCCCC--HHHHHHhhhhh-hcC-----CCCccccCCcccc
Q 030808 44 RPDFPCPYCYEDFD--IASLCSHLEDE-HSC-----ESKVTVCPICSVK 84 (171)
Q Consensus 44 r~~F~CPfC~e~fD--~~~L~~H~~ee-H~~-----e~k~vVCPVCaa~ 84 (171)
..+-.||.||.+.| +.+||.=|--+ |+. +.+..+|+-|-+.
T Consensus 4 ~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~ 52 (355)
T COG1499 4 ASTILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGAY 52 (355)
T ss_pred CcccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCCc
Confidence 35678999999887 88999888766 554 3334789999754
No 147
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=28.76 E-value=19 Score=32.65 Aligned_cols=18 Identities=22% Similarity=0.615 Sum_probs=14.4
Q ss_pred CccccCCccccchhhHHh
Q 030808 74 KVTVCPICSVKVARDMLS 91 (171)
Q Consensus 74 k~vVCPVCaa~~s~d~l~ 91 (171)
+..+||||.++|...||.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 457999999999777764
No 148
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.58 E-value=34 Score=31.52 Aligned_cols=26 Identities=27% Similarity=0.599 Sum_probs=20.9
Q ss_pred CCCCCCCcccCCCCCCCCCHHHHHHh
Q 030808 39 VEDDVRPDFPCPYCYEDFDIASLCSH 64 (171)
Q Consensus 39 ~ddd~r~~F~CPfC~e~fD~~~L~~H 64 (171)
.-+.+...|+||.|+..|-..+|-.|
T Consensus 13 ~~~q~~~~fpc~ic~r~f~~~~L~kh 38 (351)
T KOG3940|consen 13 RLAQMQMRFPCRICQREFRRRELMKH 38 (351)
T ss_pred ccccccccccccccccchhhhhhhcc
Confidence 33456789999999998888888776
No 149
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=27.67 E-value=62 Score=24.37 Aligned_cols=35 Identities=26% Similarity=0.620 Sum_probs=25.7
Q ss_pred cCCCCCC-----CCCHHHHHHhhhhhhcC------CCCccccCCccc
Q 030808 48 PCPYCYE-----DFDIASLCSHLEDEHSC------ESKVTVCPICSV 83 (171)
Q Consensus 48 ~CPfC~e-----~fD~~~L~~H~~eeH~~------e~k~vVCPVCaa 83 (171)
.||-|-. .+ +-++|.|+--.|+. .++.+-||+|..
T Consensus 33 ~Cp~Ck~PgDdCPL-v~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq 78 (84)
T KOG1493|consen 33 CCPDCKLPGDDCPL-VWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQ 78 (84)
T ss_pred cCCCCcCCCCCCcc-HHHHHHHHHHHHHHHHHhcCccccccCCcchh
Confidence 6777732 34 77899999888874 445689999964
No 150
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=27.48 E-value=37 Score=18.36 Aligned_cols=19 Identities=37% Similarity=0.522 Sum_probs=8.3
Q ss_pred ccCCCCCC-CCCHHHHHHhh
Q 030808 47 FPCPYCYE-DFDIASLCSHL 65 (171)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~ 65 (171)
|.|..|.. =-+...|..|+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCCcCCHHHHHHHH
Confidence 34444544 33344444444
No 151
>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=27.39 E-value=20 Score=25.24 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=8.2
Q ss_pred CCcccCCCCCC
Q 030808 44 RPDFPCPYCYE 54 (171)
Q Consensus 44 r~~F~CPfC~e 54 (171)
...+.|-+||+
T Consensus 3 k~~~~C~~Cg~ 13 (69)
T PF09706_consen 3 KKKYNCIFCGE 13 (69)
T ss_pred CCCCcCcCCCC
Confidence 35678999984
No 152
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=27.35 E-value=21 Score=29.83 Aligned_cols=22 Identities=18% Similarity=0.221 Sum_probs=0.0
Q ss_pred cccCCCCCCCCCHHHHHHhhhh
Q 030808 46 DFPCPYCYEDFDIASLCSHLED 67 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~e 67 (171)
...||+||+-+-+..+-+|+.-
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi 189 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRI 189 (229)
T ss_dssp ----------------------
T ss_pred cccccccccccccccccccccc
Confidence 4799999999999999999864
No 153
>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=27.04 E-value=47 Score=24.46 Aligned_cols=36 Identities=31% Similarity=0.537 Sum_probs=0.0
Q ss_pred CCCccccCCccccc-hhhHHhhhhhcccchhhhhhhc
Q 030808 72 ESKVTVCPICSVKV-ARDMLSHITLQHGHLFKLQRRR 107 (171)
Q Consensus 72 e~k~vVCPVCaa~~-s~d~l~HL~~qH~~~~k~~r~r 107 (171)
+.+.+||-.|-..| ...+.+||..+|.......++.
T Consensus 8 ~~~vlIC~~C~~av~~~~v~~HL~~~H~~~~~~~~~~ 44 (109)
T PF12013_consen 8 EYRVLICRQCQYAVQPSEVESHLRKRHHILKSQERQR 44 (109)
T ss_pred cCCEEEeCCCCcccCchHHHHHHHHhcccccHHHHHH
No 154
>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=26.84 E-value=23 Score=27.27 Aligned_cols=38 Identities=26% Similarity=0.531 Sum_probs=20.9
Q ss_pred ccCCCCCCCCCHHHHHHhhhhh-hcCC-CC-ccccCCccccchh
Q 030808 47 FPCPYCYEDFDIASLCSHLEDE-HSCE-SK-VTVCPICSVKVAR 87 (171)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~ee-H~~e-~k-~vVCPVCaa~~s~ 87 (171)
-.|||||....+ ...-+-+ |..+ .. .=+|+-|-+.|+.
T Consensus 3 ~~CpYCg~~~~l---~~~~~iYg~~~~~~~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAEL---VDGSEIYGHRYDDGPYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEE---cccchhcCccCCCCceeEECCCCCceeee
Confidence 369999883222 2222222 2221 12 2689999998754
No 155
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=26.81 E-value=23 Score=26.10 Aligned_cols=14 Identities=36% Similarity=0.698 Sum_probs=8.1
Q ss_pred CCCCcccCCCCCCC
Q 030808 42 DVRPDFPCPYCYED 55 (171)
Q Consensus 42 d~r~~F~CPfC~e~ 55 (171)
||-+.|.||-|++.
T Consensus 61 ENMs~~~Cp~Cg~~ 74 (81)
T PF10609_consen 61 ENMSYFVCPHCGER 74 (81)
T ss_dssp ECT-EEE-TTT--E
T ss_pred ECCCccCCCCCCCe
Confidence 56789999999983
No 156
>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=26.62 E-value=14 Score=28.04 Aligned_cols=29 Identities=24% Similarity=0.544 Sum_probs=18.1
Q ss_pred CCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 43 ~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
.+..+.|+-|+..|+..... ..||-|-..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~-------------~~CP~Cgs~ 95 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD-------------FSCPRCGSP 95 (113)
T ss_dssp E--EEEETTTS-EEECHHCC-------------HH-SSSSSS
T ss_pred cCCcEECCCCCCEEecCCCC-------------CCCcCCcCC
Confidence 46789999999977665433 239999775
No 157
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.36 E-value=34 Score=28.69 Aligned_cols=13 Identities=46% Similarity=0.958 Sum_probs=10.2
Q ss_pred ccCCCCCCCCCHH
Q 030808 47 FPCPYCYEDFDIA 59 (171)
Q Consensus 47 F~CPfC~e~fD~~ 59 (171)
=+||+|+.-+|-.
T Consensus 155 P~CPlCg~PlDP~ 167 (171)
T PF11290_consen 155 PPCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCCC
Confidence 4799999977743
No 158
>PF14369 zf-RING_3: zinc-finger
Probab=26.35 E-value=32 Score=21.43 Aligned_cols=9 Identities=44% Similarity=1.228 Sum_probs=7.6
Q ss_pred cCCCCCCCC
Q 030808 48 PCPYCYEDF 56 (171)
Q Consensus 48 ~CPfC~e~f 56 (171)
.||.|+.+|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 799998765
No 159
>PF08168 NUC205: NUC205 domain; InterPro: IPR012584 This domain is found in a novel family of nucleolar proteins [].; GO: 0005634 nucleus
Probab=26.34 E-value=22 Score=23.82 Aligned_cols=10 Identities=60% Similarity=0.889 Sum_probs=8.0
Q ss_pred ccccCcCCCC
Q 030808 162 QCIPETQAPI 171 (171)
Q Consensus 162 ~~~~~~~~~~ 171 (171)
-||+||.+||
T Consensus 26 GCiyetlip~ 35 (44)
T PF08168_consen 26 GCIYETLIPI 35 (44)
T ss_pred Cceeeeeccc
Confidence 3888888886
No 160
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=26.31 E-value=23 Score=34.27 Aligned_cols=21 Identities=29% Similarity=0.487 Sum_probs=16.6
Q ss_pred hhhhhcCCCCccccCCccccc
Q 030808 65 LEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 65 ~~eeH~~e~k~vVCPVCaa~~ 85 (171)
|..+...+++.-|||||..+|
T Consensus 83 c~~~~g~~PNt~vcpvclg~P 103 (544)
T PLN02751 83 CPYNYGAEPNTTVCPVCMGLP 103 (544)
T ss_pred CCcccCCCCccCcCccccCCC
Confidence 344555688999999999997
No 161
>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=26.26 E-value=37 Score=27.35 Aligned_cols=31 Identities=16% Similarity=0.320 Sum_probs=21.2
Q ss_pred CCCcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccccCCccccch
Q 030808 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (171)
Q Consensus 43 ~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s 86 (171)
+-....||-||. =+|+ ...++|||-|-....
T Consensus 6 lGtKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDL-------------NRRPAVSPYTGEQFP 37 (129)
T ss_pred hCccccCCCcCcccccc-------------CCCCccCCCcCCccC
Confidence 445678999988 4442 245789999977643
No 162
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.23 E-value=48 Score=30.74 Aligned_cols=26 Identities=27% Similarity=0.765 Sum_probs=21.5
Q ss_pred cccCCCCCCCCCHHHHHHhhhhhhcCC
Q 030808 46 DFPCPYCYEDFDIASLCSHLEDEHSCE 72 (171)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e 72 (171)
+.-||||.-.++..+.|.|++ .|--+
T Consensus 2 e~iCP~CkLsv~~~~m~~Hie-aHFEq 27 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIE-AHFEQ 27 (393)
T ss_pred cccccceecccCHHHHHHHHH-hhccc
Confidence 457999999999999999999 55443
No 163
>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=26.20 E-value=6.4 Score=29.33 Aligned_cols=21 Identities=29% Similarity=0.641 Sum_probs=15.9
Q ss_pred CcccCCCCCC-CCCHHHHHHhh
Q 030808 45 PDFPCPYCYE-DFDIASLCSHL 65 (171)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~ 65 (171)
..|.||+|.. .-.+..|.++.
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 4699999998 66677777774
No 164
>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=25.93 E-value=18 Score=27.02 Aligned_cols=7 Identities=57% Similarity=1.497 Sum_probs=3.8
Q ss_pred cCCCCCC
Q 030808 48 PCPYCYE 54 (171)
Q Consensus 48 ~CPfC~e 54 (171)
+|||||+
T Consensus 3 ~CP~CG~ 9 (84)
T PF04267_consen 3 PCPHCGP 9 (84)
T ss_dssp EETTTEE
T ss_pred cCCCCCc
Confidence 4555554
No 165
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.37 E-value=47 Score=33.17 Aligned_cols=29 Identities=31% Similarity=0.448 Sum_probs=25.3
Q ss_pred CCcccCCCCCC-CCCHHHHHHhhhhhhcCC
Q 030808 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCE 72 (171)
Q Consensus 44 r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e 72 (171)
+.---|+||.+ -||..+|..|+..+|.+.
T Consensus 180 rGhp~C~~C~~~fld~~el~rH~~~~h~~c 209 (669)
T KOG2231|consen 180 RGHPLCKFCHERFLDDDELYRHLRFDHEFC 209 (669)
T ss_pred cCCccchhhhhhhccHHHHHHhhccceehe
Confidence 44578999999 999999999999999863
No 166
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.73 E-value=22 Score=32.19 Aligned_cols=41 Identities=27% Similarity=0.536 Sum_probs=25.4
Q ss_pred CcccCCCCCC--CCCHHHH-HHhhhhhhcCCCCc-----cccCCccccc
Q 030808 45 PDFPCPYCYE--DFDIASL-CSHLEDEHSCESKV-----TVCPICSVKV 85 (171)
Q Consensus 45 ~~F~CPfC~e--~fD~~~L-~~H~~eeH~~e~k~-----vVCPVCaa~~ 85 (171)
.+-.||+||+ -+--... |.|+-=+-+..++. -.||-|.+.+
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 4678999999 3444444 77754444443332 3688887654
No 167
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=24.25 E-value=45 Score=20.56 Aligned_cols=13 Identities=23% Similarity=0.531 Sum_probs=8.4
Q ss_pred CCCCcccCCCCCC
Q 030808 42 DVRPDFPCPYCYE 54 (171)
Q Consensus 42 d~r~~F~CPfC~e 54 (171)
+......||+||-
T Consensus 13 ~~~~~irC~~CG~ 25 (32)
T PF03604_consen 13 KPGDPIRCPECGH 25 (32)
T ss_dssp STSSTSSBSSSS-
T ss_pred CCCCcEECCcCCC
Confidence 3445678998874
No 168
>PRK10220 hypothetical protein; Provisional
Probab=24.10 E-value=50 Score=26.06 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=7.7
Q ss_pred CCccccCCcccc
Q 030808 73 SKVTVCPICSVK 84 (171)
Q Consensus 73 ~k~vVCPVCaa~ 84 (171)
....|||-|+--
T Consensus 18 ~~~~vCpeC~hE 29 (111)
T PRK10220 18 NGMYICPECAHE 29 (111)
T ss_pred CCeEECCcccCc
Confidence 345777777654
No 169
>TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit. The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both.
Probab=24.06 E-value=28 Score=33.12 Aligned_cols=14 Identities=29% Similarity=0.691 Sum_probs=12.9
Q ss_pred CCCccccCCccccc
Q 030808 72 ESKVTVCPICSVKV 85 (171)
Q Consensus 72 e~k~vVCPVCaa~~ 85 (171)
+++.-|||||...|
T Consensus 34 ~PNt~v~pvclg~P 47 (478)
T TIGR00133 34 PPNTNVCPVCLGLP 47 (478)
T ss_pred CCCcccCccccCCC
Confidence 78889999999997
No 170
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=23.92 E-value=33 Score=31.90 Aligned_cols=10 Identities=60% Similarity=1.447 Sum_probs=8.7
Q ss_pred CcccCCCCCC
Q 030808 45 PDFPCPYCYE 54 (171)
Q Consensus 45 ~~F~CPfC~e 54 (171)
.+|.||||.+
T Consensus 375 ~~FKCPYCP~ 384 (396)
T COG5109 375 LSFKCPYCPE 384 (396)
T ss_pred EEeeCCCCCc
Confidence 4799999987
No 171
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=23.62 E-value=22 Score=23.32 Aligned_cols=17 Identities=41% Similarity=0.960 Sum_probs=11.0
Q ss_pred cccCCCCCC-CCCHHHHH
Q 030808 46 DFPCPYCYE-DFDIASLC 62 (171)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~ 62 (171)
.|.||+|.. .-.+..+.
T Consensus 6 d~~Cp~C~~~~~~l~~~~ 23 (98)
T cd02972 6 DPLCPYCYLFEPELEKLL 23 (98)
T ss_pred CCCCHhHHhhhHHHHHHH
Confidence 578999988 44444443
No 172
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.60 E-value=28 Score=26.65 Aligned_cols=30 Identities=27% Similarity=0.580 Sum_probs=20.6
Q ss_pred CCCcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 43 ~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
.+..+.|+-|+..+..... ....||-|.+.
T Consensus 68 vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 4668999999976655422 23459999864
No 173
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=23.53 E-value=20 Score=31.38 Aligned_cols=49 Identities=18% Similarity=0.467 Sum_probs=26.4
Q ss_pred cCCCcCCCCCCCCCcccCCCCCC--------CCCHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 32 LSIDDFEVEDDVRPDFPCPYCYE--------DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 32 ~g~e~~~~ddd~r~~F~CPfC~e--------~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
|+-++++.-+...-.|.|+ |.+ .+...+|-+=++++ +.-.++|..|..+
T Consensus 221 f~~~~~~il~~~~v~f~C~-CS~er~~~~L~~Lg~~El~~i~~e~---~~iev~C~FC~~~ 277 (293)
T PRK00114 221 YHEEDVKILEPQPVEFKCD-CSRERSANALKSLGKEELQEMIAED---GGAEMVCQFCGNK 277 (293)
T ss_pred hCCCCceeccCccCceeCC-CCHHHHHHHHHhCCHHHHHHHHHcC---CCEEEEEeCCCCE
Confidence 3434444444555678887 543 24445554433332 2335788888776
No 174
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=23.33 E-value=47 Score=29.38 Aligned_cols=47 Identities=21% Similarity=0.470 Sum_probs=25.9
Q ss_pred ccCCCCCCCC-CHHHHHHhhhhhhcCCCCccccCCccccch--hhHHhhhhh
Q 030808 47 FPCPYCYEDF-DIASLCSHLEDEHSCESKVTVCPICSVKVA--RDMLSHITL 95 (171)
Q Consensus 47 F~CPfC~e~f-D~~~L~~H~~eeH~~e~k~vVCPVCaa~~s--~d~l~HL~~ 95 (171)
+.|-|||++| |.-+|..|.... +.-++-.|.+|-.--+ -.+-.||..
T Consensus 146 ~lct~cgkgfndtfdlkrh~rth--tgvrpykc~~c~kaftqrcsleshl~k 195 (267)
T KOG3576|consen 146 HLCTFCGKGFNDTFDLKRHTRTH--TGVRPYKCSLCEKAFTQRCSLESHLKK 195 (267)
T ss_pred HHHhhccCcccchhhhhhhhccc--cCccccchhhhhHHHHhhccHHHHHHH
Confidence 6677777754 445666666543 2345566777754321 234455544
No 175
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.29 E-value=25 Score=26.88 Aligned_cols=11 Identities=18% Similarity=0.552 Sum_probs=5.3
Q ss_pred CCcccCCCCCC
Q 030808 44 RPDFPCPYCYE 54 (171)
Q Consensus 44 r~~F~CPfC~e 54 (171)
+..+.|+-|+.
T Consensus 68 p~~~~C~~Cg~ 78 (114)
T PRK03681 68 EAECWCETCQQ 78 (114)
T ss_pred CcEEEcccCCC
Confidence 34455555544
No 176
>KOG0429 consensus Ubiquitin-conjugating enzyme-related protein Ft1, involved in programmed cell death [Posttranslational modification, protein turnover, chaperones]
Probab=22.94 E-value=31 Score=30.53 Aligned_cols=18 Identities=33% Similarity=0.560 Sum_probs=14.7
Q ss_pred hhhhhhhhhhhcCCcccc
Q 030808 141 ILVQKVLHQHICGKQGTA 158 (171)
Q Consensus 141 ~~~~~~~~~~~~~~~~~~ 158 (171)
..-|.|+||+||.+.++-
T Consensus 87 vF~q~vfHP~icp~skeL 104 (258)
T KOG0429|consen 87 VFEQSVFHPLICPKSKEL 104 (258)
T ss_pred EeeccccccccCCCccce
Confidence 345789999999998873
No 177
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=22.74 E-value=62 Score=27.03 Aligned_cols=37 Identities=16% Similarity=0.398 Sum_probs=23.5
Q ss_pred cCCCCCC---CCCHHHHHHhhhhhhcCCC-CccccCCcccc
Q 030808 48 PCPYCYE---DFDIASLCSHLEDEHSCES-KVTVCPICSVK 84 (171)
Q Consensus 48 ~CPfC~e---~fD~~~L~~H~~eeH~~e~-k~vVCPVCaa~ 84 (171)
.||+|+. .++..+-..-+.+.|.... ..-+||.|-..
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 5999976 5555555555555555433 34679988775
No 178
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=22.61 E-value=56 Score=22.83 Aligned_cols=46 Identities=24% Similarity=0.499 Sum_probs=20.8
Q ss_pred CCCCcccCC--CCCCCCCHHHHHHhhhhhhcC----CCCccccCCccccchh
Q 030808 42 DVRPDFPCP--YCYEDFDIASLCSHLEDEHSC----ESKVTVCPICSVKVAR 87 (171)
Q Consensus 42 d~r~~F~CP--fC~e~fD~~~L~~H~~eeH~~----e~k~vVCPVCaa~~s~ 87 (171)
+..+...|| -|+.-|=..=|.+...+.... ....+.||.|...++-
T Consensus 16 ~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 16 GEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp -----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 334567786 888877777777777765553 3345669999887643
No 179
>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=22.49 E-value=42 Score=21.72 Aligned_cols=9 Identities=44% Similarity=1.180 Sum_probs=7.5
Q ss_pred cccCCCCCC
Q 030808 46 DFPCPYCYE 54 (171)
Q Consensus 46 ~F~CPfC~e 54 (171)
.-.||||+.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 578999985
No 180
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=22.41 E-value=60 Score=22.70 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=6.6
Q ss_pred cCCCCCCCCC
Q 030808 48 PCPYCYEDFD 57 (171)
Q Consensus 48 ~CPfC~e~fD 57 (171)
-||+||+.++
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 4788877444
No 181
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=22.03 E-value=43 Score=24.24 Aligned_cols=8 Identities=50% Similarity=1.464 Sum_probs=6.5
Q ss_pred ccCCCCCC
Q 030808 47 FPCPYCYE 54 (171)
Q Consensus 47 F~CPfC~e 54 (171)
|.||+|+.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 67999987
No 182
>PF04551 GcpE: GcpE protein; InterPro: IPR004588 This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is largely restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 0016114 terpenoid biosynthetic process, 0055114 oxidation-reduction process; PDB: 2Y0F_C 3NOY_A.
Probab=21.87 E-value=48 Score=30.76 Aligned_cols=25 Identities=28% Similarity=0.708 Sum_probs=16.6
Q ss_pred cccCCCCCC-CCCHHHHHHhhhhhhc
Q 030808 46 DFPCPYCYE-DFDIASLCSHLEDEHS 70 (171)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~ 70 (171)
.-.||-||. .||+.++..-+++.=.
T Consensus 268 ~ISCPtCGRt~~Dl~~~~~~ie~~l~ 293 (359)
T PF04551_consen 268 IISCPTCGRTEFDLQELVAEIEERLK 293 (359)
T ss_dssp EEE----TT--SHHHHHHHHHHHHCC
T ss_pred eeeCCCCCCccchHHHHHHHHHHHHh
Confidence 579999999 9999999998877544
No 183
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.66 E-value=46 Score=35.00 Aligned_cols=37 Identities=19% Similarity=0.384 Sum_probs=19.4
Q ss_pred CcccCCCCCCCCCHHHHHHhhhhhhcCCCCccccCCccccc
Q 030808 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (171)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~ 85 (171)
..|.||.||+.-...--|..|. .......||-|-..+
T Consensus 637 ~~frCP~CG~~Te~i~fCP~CG----~~~~~y~CPKCG~El 673 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRCG----IEVEEDECEKCGREP 673 (1121)
T ss_pred CcccCCCCCCCCCcceeCcccc----CcCCCCcCCCCCCCC
Confidence 3466666666433344455552 222234577776654
No 184
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=21.17 E-value=47 Score=29.50 Aligned_cols=42 Identities=17% Similarity=0.355 Sum_probs=28.1
Q ss_pred ccCCCCCCC-CCHHHHHHhhhhhhcCCCCccccCCccccchhhHHhhhhhcccc
Q 030808 47 FPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHGH 99 (171)
Q Consensus 47 F~CPfC~e~-fD~~~L~~H~~eeH~~e~k~vVCPVCaa~~s~d~l~HL~~qH~~ 99 (171)
..||.|+.. +. . -++....||--|-.-+..+.+.+-.--+.|
T Consensus 2 ~~CpeCg~~~~~---------~--d~~~ge~VC~~CG~Vi~~~~id~gpewr~f 44 (285)
T COG1405 2 MSCPECGSTNII---------T--DYERGEIVCADCGLVLEDSLIDPGPEWRAF 44 (285)
T ss_pred CCCCCCCCccce---------e--eccCCeEEeccCCEEeccccccCCCCcccc
Confidence 369999884 21 1 123567899999998877777655444444
No 185
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=20.32 E-value=28 Score=33.36 Aligned_cols=33 Identities=24% Similarity=0.545 Sum_probs=28.1
Q ss_pred CcccCCCCCC-CCCHHHHHHhhhhhhcCCCCccc
Q 030808 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTV 77 (171)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vV 77 (171)
+.|+|-||-. =+.-.+|-.|++.-|+.|.++|.
T Consensus 457 q~f~~ky~~atfyss~~ltrhin~~Hpse~rqv~ 490 (500)
T KOG3993|consen 457 QGFTCKYCPATFYSSPGLTRHINKCHPSELRQVA 490 (500)
T ss_pred hccccccchHhhhcCcchHhHhhhcChHHhhhhH
Confidence 5799999977 77888899999999999988874
No 186
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.01 E-value=38 Score=33.97 Aligned_cols=40 Identities=23% Similarity=0.402 Sum_probs=28.0
Q ss_pred CCCcccCCCCCCCC----CHHHHHHhhhhhhcCCCCccccCCcccc
Q 030808 43 VRPDFPCPYCYEDF----DIASLCSHLEDEHSCESKVTVCPICSVK 84 (171)
Q Consensus 43 ~r~~F~CPfC~e~f----D~~~L~~H~~eeH~~e~k~vVCPVCaa~ 84 (171)
....+.||.|+..+ +...|.||--..+ +..+-.||=|-+.
T Consensus 441 Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 441 CGYIAECPNCDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred CCCcccCCCCCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 34578999997733 3356666655444 5677899999886
Done!