Query 028852
Match_columns 202
No_of_seqs 146 out of 210
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 03:33:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028852.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028852hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14571 Di19_C: Stress-induce 99.9 5.3E-23 1.2E-27 159.6 6.0 77 119-199 1-105 (105)
2 PF05605 zf-Di19: Drought indu 99.8 6.1E-20 1.3E-24 125.9 3.5 54 45-98 1-54 (54)
3 KOG1280 Uncharacterized conser 98.6 4E-08 8.7E-13 90.2 3.8 57 27-85 61-119 (381)
4 PF09237 GAGA: GAGA factor; I 95.4 0.01 2.2E-07 41.4 1.9 27 73-99 22-50 (54)
5 KOG2923 Uncharacterized conser 95.0 0.014 3.1E-07 42.3 1.8 46 31-85 6-54 (67)
6 COG5216 Uncharacterized conser 94.7 0.013 2.8E-07 42.1 0.9 45 32-85 7-54 (67)
7 PF13894 zf-C2H2_4: C2H2-type 93.9 0.024 5.3E-07 31.0 0.7 23 47-69 1-24 (24)
8 PLN03086 PRLI-interacting fact 92.9 0.098 2.1E-06 51.5 3.6 50 42-96 449-499 (567)
9 PF13913 zf-C2HC_2: zinc-finge 92.9 0.065 1.4E-06 31.6 1.5 21 46-66 2-22 (25)
10 PF12756 zf-C2H2_2: C2H2 type 91.9 0.099 2.2E-06 37.6 1.7 49 48-96 1-73 (100)
11 PF14354 Lar_restr_allev: Rest 91.1 0.1 2.2E-06 35.8 1.0 31 46-83 3-37 (61)
12 PHA00733 hypothetical protein 91.1 0.28 6E-06 39.2 3.7 51 45-99 72-125 (128)
13 PHA00732 hypothetical protein 91.0 0.24 5.2E-06 36.7 3.0 42 47-93 2-44 (79)
14 smart00531 TFIIE Transcription 90.8 0.21 4.5E-06 40.5 2.7 39 42-85 95-133 (147)
15 PF00096 zf-C2H2: Zinc finger, 90.6 0.073 1.6E-06 29.6 -0.0 21 47-67 1-22 (23)
16 PRK09710 lar restriction allev 90.3 0.12 2.7E-06 37.4 0.9 30 46-84 6-36 (64)
17 PF08271 TF_Zn_Ribbon: TFIIB z 90.3 0.11 2.5E-06 33.8 0.6 34 47-90 1-34 (43)
18 KOG2462 C2H2-type Zn-finger pr 90.0 0.28 6E-06 44.5 3.1 37 44-84 159-196 (279)
19 KOG2462 C2H2-type Zn-finger pr 89.0 0.32 7E-06 44.1 2.7 40 44-84 128-170 (279)
20 TIGR02098 MJ0042_CXXC MJ0042 f 89.0 0.24 5.2E-06 31.1 1.4 33 46-84 2-34 (38)
21 TIGR01206 lysW lysine biosynth 88.9 0.19 4.2E-06 35.0 0.9 31 46-85 2-32 (54)
22 PF13909 zf-H2C2_5: C2H2-type 88.7 0.14 3E-06 29.0 0.1 24 47-70 1-24 (24)
23 PLN03208 E3 ubiquitin-protein 88.6 0.22 4.7E-06 43.0 1.3 45 44-88 16-81 (193)
24 PLN03086 PRLI-interacting fact 88.2 0.38 8.2E-06 47.5 2.8 37 46-85 478-514 (567)
25 PRK14892 putative transcriptio 87.6 0.25 5.4E-06 38.4 1.0 37 43-87 18-54 (99)
26 PHA02768 hypothetical protein; 86.2 0.49 1.1E-05 33.2 1.8 35 46-84 5-40 (55)
27 PF09986 DUF2225: Uncharacteri 86.0 0.29 6.3E-06 42.1 0.6 18 46-63 5-22 (214)
28 smart00834 CxxC_CXXC_SSSS Puta 85.9 0.26 5.6E-06 31.0 0.2 33 45-85 4-36 (41)
29 COG4888 Uncharacterized Zn rib 83.8 0.32 6.9E-06 38.2 -0.1 36 44-84 20-55 (104)
30 PF08274 PhnA_Zn_Ribbon: PhnA 83.8 0.49 1.1E-05 29.4 0.7 24 48-83 4-27 (30)
31 COG1655 Uncharacterized protei 83.0 0.56 1.2E-05 42.0 1.1 13 45-57 18-30 (267)
32 PF14206 Cys_rich_CPCC: Cystei 82.6 0.65 1.4E-05 34.7 1.1 27 46-83 1-28 (78)
33 cd00350 rubredoxin_like Rubred 81.4 0.69 1.5E-05 28.7 0.8 24 47-83 2-25 (33)
34 smart00734 ZnF_Rad18 Rad18-lik 80.2 1.1 2.5E-05 26.6 1.4 19 48-66 3-21 (26)
35 TIGR02605 CxxC_CxxC_SSSS putat 80.0 1 2.2E-05 30.0 1.3 31 45-83 4-34 (52)
36 PF14255 Cys_rich_CPXG: Cystei 79.7 0.65 1.4E-05 32.2 0.3 34 47-85 1-34 (52)
37 PRK00398 rpoP DNA-directed RNA 78.5 0.76 1.7E-05 30.2 0.3 29 46-85 3-31 (46)
38 PF02176 zf-TRAF: TRAF-type zi 78.2 0.93 2E-05 30.5 0.7 46 45-92 8-60 (60)
39 PRK14890 putative Zn-ribbon RN 77.3 1.6 3.5E-05 31.1 1.7 33 43-82 22-55 (59)
40 KOG2593 Transcription initiati 77.2 1.5 3.3E-05 42.1 2.0 63 34-103 116-192 (436)
41 smart00504 Ubox Modified RING 77.2 2 4.4E-05 28.8 2.1 33 47-86 2-46 (63)
42 KOG1842 FYVE finger-containing 77.1 1.2 2.5E-05 43.2 1.2 34 41-74 10-44 (505)
43 PF05129 Elf1: Transcription e 76.7 1.1 2.3E-05 33.5 0.7 34 44-84 20-55 (81)
44 KOG3623 Homeobox transcription 76.1 0.73 1.6E-05 47.1 -0.4 52 44-95 208-262 (1007)
45 PF12756 zf-C2H2_2: C2H2 type 76.0 1 2.2E-05 32.2 0.4 26 45-70 49-75 (100)
46 PF03470 zf-XS: XS zinc finger 74.4 1.9 4.2E-05 28.9 1.4 9 56-64 12-20 (43)
47 cd00729 rubredoxin_SM Rubredox 74.3 1.4 3E-05 27.7 0.7 26 46-84 2-27 (34)
48 PF13912 zf-C2H2_6: C2H2-type 74.3 1.6 3.5E-05 25.0 0.9 23 47-69 2-25 (27)
49 PF03145 Sina: Seven in absent 73.2 1.7 3.8E-05 36.3 1.2 54 45-101 13-75 (198)
50 COG2888 Predicted Zn-ribbon RN 72.2 3.4 7.4E-05 29.7 2.3 34 42-82 23-57 (61)
51 PF04564 U-box: U-box domain; 71.9 3.6 7.8E-05 29.4 2.4 38 44-87 2-51 (73)
52 PRK12495 hypothetical protein; 71.8 2.5 5.3E-05 37.4 1.8 31 44-87 40-70 (226)
53 PF07754 DUF1610: Domain of un 71.8 2.1 4.6E-05 25.3 1.0 12 43-54 13-24 (24)
54 PRK06266 transcription initiat 71.6 3 6.4E-05 35.2 2.2 33 43-85 114-146 (178)
55 TIGR03655 anti_R_Lar restricti 70.8 1.9 4E-05 29.3 0.7 33 47-84 2-35 (53)
56 PTZ00255 60S ribosomal protein 70.5 1.3 2.9E-05 34.0 -0.1 32 42-85 32-64 (90)
57 TIGR00373 conserved hypothetic 70.0 3.4 7.4E-05 34.0 2.2 34 42-85 105-138 (158)
58 smart00355 ZnF_C2H2 zinc finge 69.7 3.4 7.3E-05 22.1 1.5 20 47-66 1-21 (26)
59 PF04780 DUF629: Protein of un 69.2 2.8 6.1E-05 40.6 1.7 42 43-84 54-99 (466)
60 PHA00616 hypothetical protein 69.1 2 4.3E-05 28.9 0.5 25 47-71 2-27 (44)
61 KOG0320 Predicted E3 ubiquitin 68.7 2.6 5.7E-05 36.3 1.3 44 44-87 129-179 (187)
62 PF13719 zinc_ribbon_5: zinc-r 67.9 4.2 9E-05 25.8 1.8 31 46-84 2-34 (37)
63 PF13465 zf-H2C2_2: Zinc-finge 66.8 1.2 2.7E-05 25.9 -0.7 11 46-56 14-24 (26)
64 PF07191 zinc-ribbons_6: zinc- 66.6 0.67 1.4E-05 34.1 -2.3 54 47-104 2-62 (70)
65 PF09723 Zn-ribbon_8: Zinc rib 66.0 1.7 3.6E-05 28.3 -0.3 31 45-83 4-34 (42)
66 PF15616 TerY-C: TerY-C metal 65.6 2.8 6E-05 34.2 0.8 42 46-89 77-119 (131)
67 smart00659 RPOLCX RNA polymera 65.0 3.8 8.3E-05 27.2 1.3 28 46-85 2-29 (44)
68 KOG2932 E3 ubiquitin ligase in 64.7 3 6.5E-05 39.0 0.9 58 46-103 90-177 (389)
69 TIGR00280 L37a ribosomal prote 64.5 1.9 4E-05 33.3 -0.4 32 42-85 31-63 (91)
70 COG0675 Transposase and inacti 64.5 5.9 0.00013 33.9 2.6 45 33-93 296-340 (364)
71 PF05605 zf-Di19: Drought indu 64.5 3.9 8.4E-05 27.6 1.2 24 46-70 31-54 (54)
72 PF12773 DZR: Double zinc ribb 64.4 4.5 9.9E-05 26.4 1.5 29 46-86 12-40 (50)
73 PF07282 OrfB_Zn_ribbon: Putat 63.3 9.3 0.0002 26.5 3.1 47 33-91 16-62 (69)
74 PRK00420 hypothetical protein; 63.2 5.3 0.00012 31.7 2.0 28 46-85 23-50 (112)
75 PF14353 CpXC: CpXC protein 62.4 3.1 6.8E-05 32.4 0.5 37 47-85 2-48 (128)
76 PRK03976 rpl37ae 50S ribosomal 62.2 2.3 4.9E-05 32.7 -0.3 32 42-85 32-64 (90)
77 TIGR00100 hypA hydrogenase nic 61.8 2.7 5.8E-05 32.9 0.0 30 42-84 66-95 (115)
78 COG5175 MOT2 Transcriptional r 61.3 3.5 7.5E-05 39.1 0.7 35 49-84 17-62 (480)
79 COG1592 Rubrerythrin [Energy p 60.5 5.3 0.00011 33.8 1.6 25 46-84 134-158 (166)
80 COG5189 SFP1 Putative transcri 59.9 4.7 0.0001 37.9 1.3 40 46-85 349-408 (423)
81 PF11672 DUF3268: Protein of u 59.8 5.5 0.00012 31.1 1.5 38 47-87 3-43 (102)
82 COG1645 Uncharacterized Zn-fin 59.8 4.9 0.00011 32.8 1.3 26 46-84 28-53 (131)
83 PRK12496 hypothetical protein; 59.3 6.5 0.00014 32.6 2.0 28 46-86 127-154 (164)
84 COG4311 SoxD Sarcosine oxidase 58.7 4.4 9.4E-05 31.6 0.7 9 46-54 3-11 (97)
85 PF10571 UPF0547: Uncharacteri 58.7 6.1 0.00013 23.6 1.2 8 49-56 3-10 (26)
86 PF13395 HNH_4: HNH endonuclea 57.7 5.9 0.00013 26.8 1.2 14 49-62 1-14 (54)
87 PF08996 zf-DNA_Pol: DNA Polym 57.5 2.7 5.9E-05 35.3 -0.6 40 44-85 16-55 (188)
88 COG4049 Uncharacterized protei 57.0 4.6 9.9E-05 29.0 0.6 27 75-101 17-45 (65)
89 PF11789 zf-Nse: Zinc-finger o 57.0 9.6 0.00021 26.5 2.2 33 43-80 8-53 (57)
90 PF09538 FYDLN_acid: Protein o 56.8 9.1 0.0002 30.0 2.3 33 42-87 5-38 (108)
91 PF08209 Sgf11: Sgf11 (transcr 55.8 4.3 9.3E-05 25.7 0.2 18 76-93 5-23 (33)
92 smart00507 HNHc HNH nucleases. 55.1 3.8 8.3E-05 25.5 -0.1 21 47-67 11-31 (52)
93 PF14446 Prok-RING_1: Prokaryo 54.9 9.1 0.0002 26.8 1.8 27 46-85 5-31 (54)
94 PF04981 NMD3: NMD3 family ; 52.4 9.8 0.00021 33.0 2.0 36 49-84 1-44 (236)
95 PRK12380 hydrogenase nickel in 52.4 5 0.00011 31.3 0.2 30 42-84 66-95 (113)
96 PRK03824 hypA hydrogenase nick 52.2 6 0.00013 31.9 0.6 43 42-84 66-116 (135)
97 PF13240 zinc_ribbon_2: zinc-r 51.8 6.1 0.00013 22.8 0.4 6 49-54 2-7 (23)
98 COG5236 Uncharacterized conser 51.8 8.2 0.00018 36.8 1.5 55 44-104 218-312 (493)
99 PRK11088 rrmA 23S rRNA methylt 50.9 6.1 0.00013 34.3 0.5 26 46-71 2-27 (272)
100 cd00730 rubredoxin Rubredoxin; 50.1 8.5 0.00018 26.3 1.0 14 41-54 29-42 (50)
101 PF13248 zf-ribbon_3: zinc-rib 49.8 11 0.00023 22.1 1.2 9 47-55 3-11 (26)
102 PF01780 Ribosomal_L37ae: Ribo 49.6 6.4 0.00014 30.2 0.4 32 42-85 31-63 (90)
103 TIGR00686 phnA alkylphosphonat 49.3 8.9 0.00019 30.5 1.1 25 48-84 4-28 (109)
104 PF12171 zf-C2H2_jaz: Zinc-fin 49.1 13 0.00028 21.4 1.6 20 47-66 2-22 (27)
105 PF13717 zinc_ribbon_4: zinc-r 49.0 14 0.0003 23.4 1.8 31 47-83 3-33 (36)
106 TIGR00570 cdk7 CDK-activating 48.5 9.3 0.0002 35.3 1.3 39 46-85 3-53 (309)
107 PF00301 Rubredoxin: Rubredoxi 48.1 8.7 0.00019 26.0 0.8 14 41-54 29-42 (47)
108 PRK03922 hypothetical protein; 47.6 9.2 0.0002 30.6 1.0 14 46-59 49-62 (113)
109 PF09706 Cas_CXXC_CXXC: CRISPR 47.3 8.2 0.00018 27.8 0.6 14 71-84 47-60 (69)
110 PF12660 zf-TFIIIC: Putative z 47.0 6.3 0.00014 30.2 -0.0 38 48-85 16-65 (99)
111 PF14634 zf-RING_5: zinc-RING 46.7 11 0.00024 24.2 1.1 10 73-82 34-43 (44)
112 KOG3214 Uncharacterized Zn rib 46.5 9.3 0.0002 30.2 0.8 37 44-85 21-57 (109)
113 PF04423 Rad50_zn_hook: Rad50 46.2 6.5 0.00014 26.5 -0.1 13 48-60 22-34 (54)
114 smart00661 RPOL9 RNA polymeras 45.9 13 0.00028 24.3 1.3 28 48-84 2-29 (52)
115 KOG2879 Predicted E3 ubiquitin 45.7 8.4 0.00018 35.3 0.6 42 44-85 237-286 (298)
116 PF14616 DUF4451: Domain of un 45.5 14 0.00031 29.4 1.7 28 75-102 25-57 (124)
117 PRK11595 DNA utilization prote 45.4 10 0.00022 32.5 1.0 34 48-83 7-42 (227)
118 PF04475 DUF555: Protein of un 45.4 10 0.00023 29.8 0.9 14 46-59 47-60 (102)
119 smart00451 ZnF_U1 U1-like zinc 45.0 14 0.00031 21.9 1.4 21 46-66 3-24 (35)
120 PF10058 DUF2296: Predicted in 44.9 9.8 0.00021 26.3 0.7 10 45-54 43-52 (54)
121 PF01155 HypA: Hydrogenase exp 44.9 4.8 0.0001 31.3 -1.0 30 42-84 66-95 (113)
122 PRK05477 gatB aspartyl/glutamy 44.7 11 0.00024 36.6 1.2 22 65-86 27-48 (474)
123 PF02146 SIR2: Sir2 family; I 44.2 8.6 0.00019 31.4 0.4 41 45-90 104-144 (178)
124 COG1198 PriA Primosomal protei 44.1 13 0.00029 37.9 1.7 41 42-84 440-484 (730)
125 PF12230 PRP21_like_P: Pre-mRN 43.3 7.9 0.00017 33.2 0.0 38 75-112 168-207 (229)
126 PF02892 zf-BED: BED zinc fing 42.9 18 0.00039 22.9 1.7 26 72-97 13-44 (45)
127 COG1499 NMD3 NMD protein affec 42.8 14 0.00031 34.5 1.6 40 44-83 4-51 (355)
128 PRK00423 tfb transcription ini 42.7 15 0.00031 33.3 1.6 40 43-92 8-47 (310)
129 PF14279 HNH_5: HNH endonuclea 42.3 8.7 0.00019 27.9 0.1 44 49-93 1-48 (71)
130 PF12760 Zn_Tnp_IS1595: Transp 41.7 15 0.00033 24.0 1.2 11 44-54 16-26 (46)
131 KOG4628 Predicted E3 ubiquitin 41.2 9.1 0.0002 35.9 0.1 39 47-85 230-277 (348)
132 COG1675 TFA1 Transcription ini 40.9 14 0.00031 31.5 1.2 32 44-85 111-142 (176)
133 KOG0823 Predicted E3 ubiquitin 40.4 12 0.00026 33.3 0.7 45 44-88 45-97 (230)
134 KOG0402 60S ribosomal protein 40.2 8.5 0.00018 29.6 -0.2 16 42-57 32-48 (92)
135 PF09862 DUF2089: Protein of u 40.0 12 0.00025 29.8 0.5 64 49-120 1-66 (113)
136 PF13824 zf-Mss51: Zinc-finger 40.0 15 0.00033 25.8 1.0 11 44-54 12-22 (55)
137 TIGR03830 CxxCG_CxxCG_HTH puta 39.5 13 0.00028 28.2 0.7 37 49-85 1-41 (127)
138 PLN02751 glutamyl-tRNA(Gln) am 39.5 14 0.00031 36.5 1.1 22 65-86 83-104 (544)
139 COG1405 SUA7 Transcription ini 39.4 18 0.0004 32.8 1.7 43 47-99 2-44 (285)
140 KOG3608 Zn finger proteins [Ge 39.1 25 0.00055 33.6 2.6 49 45-94 262-313 (467)
141 PF00097 zf-C3HC4: Zinc finger 39.1 3.8 8.2E-05 25.4 -2.0 9 73-81 33-41 (41)
142 TIGR02300 FYDLN_acid conserved 39.1 21 0.00046 29.1 1.9 31 42-85 5-36 (129)
143 PRK04023 DNA polymerase II lar 39.0 19 0.00041 38.4 1.9 36 46-85 638-673 (1121)
144 PF06957 COPI_C: Coatomer (COP 38.6 12 0.00026 35.9 0.5 33 45-90 379-412 (422)
145 PF11793 FANCL_C: FANCL C-term 38.5 18 0.00039 25.8 1.3 46 42-87 16-67 (70)
146 PRK00564 hypA hydrogenase nick 38.5 12 0.00027 29.3 0.4 31 42-84 67-97 (117)
147 TIGR00133 gatB glutamyl-tRNA(G 37.2 17 0.00036 35.4 1.1 15 72-86 34-48 (478)
148 PF04780 DUF629: Protein of un 36.8 13 0.00029 36.1 0.4 48 55-102 20-86 (466)
149 KOG2177 Predicted E3 ubiquitin 36.7 10 0.00022 30.7 -0.3 38 45-82 12-54 (386)
150 PF02934 GatB_N: GatB/GatE cat 36.4 19 0.0004 33.0 1.3 26 61-86 18-43 (289)
151 TIGR00515 accD acetyl-CoA carb 36.3 22 0.00047 32.3 1.7 29 46-84 26-54 (285)
152 PF09334 tRNA-synt_1g: tRNA sy 36.3 15 0.00032 34.4 0.6 40 46-85 136-176 (391)
153 PF05876 Terminase_GpA: Phage 36.1 21 0.00046 34.9 1.7 42 44-87 198-241 (557)
154 TIGR01374 soxD sarcosine oxida 35.6 18 0.00038 27.5 0.8 8 47-54 2-9 (84)
155 CHL00174 accD acetyl-CoA carbo 35.5 22 0.00047 32.7 1.6 29 46-84 38-66 (296)
156 PRK05654 acetyl-CoA carboxylas 35.4 22 0.00048 32.3 1.6 29 46-84 27-55 (292)
157 COG1997 RPL43A Ribosomal prote 35.0 8.5 0.00018 29.6 -1.0 33 40-84 29-62 (89)
158 PRK14714 DNA polymerase II lar 34.8 24 0.00052 38.4 1.9 34 46-84 667-701 (1337)
159 KOG2817 Predicted E3 ubiquitin 34.0 21 0.00046 34.0 1.3 15 45-59 373-387 (394)
160 TIGR03278 methan_mark_10 putat 33.6 19 0.00042 34.1 1.0 33 46-84 10-45 (404)
161 KOG3608 Zn finger proteins [Ge 33.6 23 0.00051 33.9 1.5 42 60-101 336-380 (467)
162 PF04267 SoxD: Sarcosine oxida 33.6 10 0.00022 28.7 -0.7 7 48-54 3-9 (84)
163 PF03966 Trm112p: Trm112p-like 33.1 28 0.0006 24.5 1.5 39 45-83 6-61 (68)
164 PHA02929 N1R/p28-like protein; 32.8 13 0.00027 33.1 -0.4 42 44-85 172-226 (238)
165 TIGR01405 polC_Gram_pos DNA po 31.9 34 0.00073 37.0 2.5 46 32-85 672-718 (1213)
166 PHA02565 49 recombination endo 31.9 23 0.0005 29.8 1.0 40 46-85 20-65 (157)
167 KOG3576 Ovo and related transc 31.8 21 0.00046 31.8 0.9 53 45-98 116-170 (267)
168 PF12230 PRP21_like_P: Pre-mRN 31.3 16 0.00035 31.3 0.0 23 46-68 168-190 (229)
169 PF14311 DUF4379: Domain of un 30.5 30 0.00064 23.3 1.2 32 42-81 24-55 (55)
170 PRK03681 hypA hydrogenase nick 30.5 16 0.00036 28.5 -0.1 31 42-84 66-96 (114)
171 PF13453 zf-TFIIB: Transcripti 30.3 19 0.00042 22.9 0.3 28 48-84 1-28 (41)
172 KOG0804 Cytoplasmic Zn-finger 30.2 14 0.0003 36.0 -0.6 37 45-83 174-219 (493)
173 PHA00733 hypothetical protein 30.1 34 0.00073 27.3 1.7 25 46-70 99-124 (128)
174 PF11290 DUF3090: Protein of u 30.1 26 0.00057 29.8 1.1 13 47-59 155-167 (171)
175 PRK00464 nrdR transcriptional 29.9 23 0.0005 29.4 0.7 32 47-85 1-38 (154)
176 COG3058 FdhE Uncharacterized p 29.8 18 0.0004 33.3 0.2 18 74-91 184-201 (308)
177 KOG1002 Nucleotide excision re 29.8 21 0.00045 35.9 0.5 54 40-93 530-593 (791)
178 PF09855 DUF2082: Nucleic-acid 29.6 19 0.0004 25.9 0.1 36 47-83 1-44 (64)
179 PF14369 zf-RING_3: zinc-finge 29.2 27 0.00058 22.1 0.8 9 48-56 23-31 (35)
180 PRK00448 polC DNA polymerase I 28.9 40 0.00087 37.1 2.5 46 32-85 897-943 (1437)
181 COG1656 Uncharacterized conser 28.7 41 0.00089 28.6 2.0 41 47-87 98-144 (165)
182 PRK09678 DNA-binding transcrip 28.6 26 0.00056 25.8 0.7 8 47-54 2-9 (72)
183 COG5109 Uncharacterized conser 28.5 24 0.00052 33.2 0.7 10 45-54 375-384 (396)
184 COG4391 Uncharacterized protei 28.5 30 0.00065 25.0 1.0 13 72-84 45-57 (62)
185 KOG4727 U1-like Zn-finger prot 28.0 26 0.00055 30.3 0.7 20 76-95 76-97 (193)
186 PF10276 zf-CHCC: Zinc-finger 28.0 21 0.00045 23.5 0.1 9 46-54 29-37 (40)
187 KOG4602 Nanos and related prot 27.9 21 0.00045 32.7 0.1 43 42-84 229-277 (318)
188 KOG3940 Uncharacterized conser 27.8 37 0.00081 31.8 1.7 24 41-64 15-38 (351)
189 KOG1074 Transcriptional repres 27.8 23 0.00051 37.0 0.5 53 46-100 353-408 (958)
190 PRK10220 hypothetical protein; 27.7 38 0.00083 27.0 1.6 26 47-84 4-29 (111)
191 smart00614 ZnF_BED BED zinc fi 27.6 25 0.00055 23.2 0.5 12 45-56 17-28 (50)
192 cd02972 DsbA_family DsbA famil 26.7 18 0.00039 24.6 -0.4 17 46-62 6-23 (98)
193 PF12874 zf-met: Zinc-finger o 26.3 29 0.00063 19.1 0.5 17 77-93 2-20 (25)
194 KOG4696 Uncharacterized conser 26.3 31 0.00067 32.4 0.9 24 46-70 2-25 (393)
195 PF05207 zf-CSL: CSL zinc fing 26.1 20 0.00044 24.6 -0.2 45 33-86 4-51 (55)
196 KOG2231 Predicted E3 ubiquitin 26.1 45 0.00097 34.0 2.1 29 44-72 180-209 (669)
197 PF14968 CCDC84: Coiled coil p 25.9 33 0.00072 32.0 1.1 25 42-66 54-85 (336)
198 KOG3623 Homeobox transcription 25.8 37 0.00081 35.3 1.5 54 42-97 277-333 (1007)
199 cd03019 DsbA_DsbA DsbA family, 25.7 27 0.00058 27.4 0.4 19 45-63 23-42 (178)
200 PRK05978 hypothetical protein; 25.7 29 0.00062 28.8 0.6 28 46-84 33-61 (148)
201 PRK00762 hypA hydrogenase nick 25.4 28 0.00061 27.6 0.4 13 43-56 67-79 (124)
202 PF13462 Thioredoxin_4: Thiore 25.3 7 0.00015 30.1 -3.0 21 45-65 20-41 (162)
203 KOG1493 Anaphase-promoting com 24.3 38 0.00082 25.7 0.9 37 46-83 31-78 (84)
204 TIGR00630 uvra excinuclease AB 24.1 45 0.00097 35.0 1.7 35 45-84 249-283 (924)
205 TIGR00595 priA primosomal prot 24.0 38 0.00081 32.8 1.1 37 46-84 222-262 (505)
206 COG5415 Predicted integral mem 24.0 74 0.0016 28.5 2.8 35 42-85 188-224 (251)
207 PF06676 DUF1178: Protein of u 23.9 39 0.00084 28.1 1.0 11 74-84 31-41 (148)
208 cd01407 SIR2-fam SIR2 family o 23.8 48 0.001 28.1 1.6 40 45-89 108-147 (218)
209 PF03604 DNA_RNApol_7kD: DNA d 23.7 45 0.00097 20.8 1.0 12 43-54 14-25 (32)
210 COG1885 Uncharacterized protei 23.7 41 0.0009 26.8 1.1 15 46-60 49-63 (115)
211 PF12013 DUF3505: Protein of u 23.6 63 0.0014 24.4 2.1 36 72-107 8-44 (109)
212 PHA02942 putative transposase; 23.5 60 0.0013 30.4 2.3 51 32-95 312-362 (383)
213 COG1281 Disulfide bond chapero 23.4 21 0.00046 32.7 -0.7 10 75-84 266-275 (286)
214 KOG4080 Mitochondrial ribosoma 23.4 34 0.00073 29.3 0.6 27 45-87 92-118 (176)
215 KOG3576 Ovo and related transc 23.3 36 0.00078 30.4 0.7 51 46-98 145-198 (267)
216 PF08273 Prim_Zn_Ribbon: Zinc- 23.2 35 0.00076 22.3 0.5 7 48-54 5-11 (40)
217 PRK02539 hypothetical protein; 23.2 77 0.0017 24.2 2.4 22 170-194 19-40 (85)
218 PRK14559 putative protein seri 23.0 51 0.0011 33.3 1.8 39 46-87 15-53 (645)
219 TIGR00244 transcriptional regu 22.9 36 0.00079 28.3 0.7 31 48-85 2-38 (147)
220 PRK13945 formamidopyrimidine-D 22.9 51 0.0011 29.4 1.6 27 47-82 255-281 (282)
221 KOG0978 E3 ubiquitin ligase in 22.8 20 0.00043 36.6 -1.0 46 43-88 640-691 (698)
222 PF09889 DUF2116: Uncharacteri 22.6 47 0.001 23.6 1.1 10 48-57 5-14 (59)
223 PHA02540 61 DNA primase; Provi 22.6 37 0.00081 31.6 0.8 10 45-54 26-35 (337)
224 TIGR00599 rad18 DNA repair pro 22.6 27 0.00058 33.3 -0.2 44 42-85 22-70 (397)
225 PRK05452 anaerobic nitric oxid 22.5 46 0.00099 32.0 1.4 10 43-52 422-431 (479)
226 COG2835 Uncharacterized conser 22.1 35 0.00077 24.4 0.4 9 44-52 6-14 (60)
227 cd03024 DsbA_FrnE DsbA family, 22.0 22 0.00048 28.6 -0.8 22 44-65 4-26 (201)
228 PRK14714 DNA polymerase II lar 21.8 54 0.0012 35.9 1.8 41 45-85 678-719 (1337)
229 COG2331 Uncharacterized protei 21.7 24 0.00053 26.6 -0.5 46 45-103 11-56 (82)
230 PF04641 Rtf2: Rtf2 RING-finge 21.5 27 0.00058 30.8 -0.4 44 42-85 109-160 (260)
231 PF06221 zf-C2HC5: Putative zi 21.5 47 0.001 23.4 0.9 9 46-54 35-43 (57)
232 COG5574 PEX10 RING-finger-cont 21.0 23 0.00049 32.3 -1.0 43 45-87 214-263 (271)
233 PF12861 zf-Apc11: Anaphase-pr 20.8 41 0.00089 25.6 0.5 36 48-83 34-79 (85)
234 PRK01546 hypothetical protein; 20.7 94 0.002 23.4 2.4 22 170-194 20-41 (79)
235 PRK03564 formate dehydrogenase 20.6 47 0.001 30.6 1.0 10 45-54 186-195 (309)
236 PF05502 Dynactin_p62: Dynacti 20.6 53 0.0012 31.8 1.4 40 44-83 50-94 (483)
237 cd03021 DsbA_GSTK DsbA family, 20.5 17 0.00037 30.3 -1.8 13 43-55 5-17 (209)
238 PF05280 FlhC: Flagellar trans 20.4 44 0.00095 28.3 0.7 11 43-53 151-161 (175)
239 cd03023 DsbA_Com1_like DsbA fa 20.3 35 0.00075 25.7 0.0 10 45-54 13-22 (154)
240 PHA02776 E7 protein; Provision 20.3 25 0.00054 27.5 -0.8 38 47-84 59-100 (101)
241 PF05180 zf-DNL: DNL zinc fing 20.2 16 0.00035 26.5 -1.7 32 46-84 4-38 (66)
242 KOG1705 Uncharacterized conser 20.2 39 0.00085 26.5 0.3 36 47-83 28-63 (110)
243 TIGR00627 tfb4 transcription f 20.2 40 0.00087 30.5 0.4 8 76-83 270-277 (279)
244 PRK00241 nudC NADH pyrophospha 20.0 59 0.0013 28.7 1.4 28 46-84 99-126 (256)
No 1
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=99.88 E-value=5.3e-23 Score=159.63 Aligned_cols=77 Identities=45% Similarity=0.601 Sum_probs=59.0
Q ss_pred hHhhhchhHHhhhhhhhhccc--ccc-cCCCC-------------------------CCcccCccccCCCccccccCCCC
Q 028852 119 ALSLLGRDLREAHLQVLLGEA--EEI-SKSVV-------------------------TSTEDTSAKSAAPTHMWKTSFDP 170 (202)
Q Consensus 119 tlSlL~Kelre~~lqsllg~~--~~~-s~~~~-------------------------~~~e~~~~~~~s~~~~~~~~~~~ 170 (202)
|||||+|||||||||+||||. ... +.++. ++.++.+.++...++.|++++++
T Consensus 1 tlsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~s~~~ 80 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSEEKKSSKKSSSEQNVKSSADS 80 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCccccccCCccccccccccccccchhcccccccCC
Confidence 789999999999999999986 211 11111 11222334445667788888899
Q ss_pred CCCHHHHHHHHhcccchhhhHHHHHhhhc
Q 028852 171 SLSHEEREKRIRQGAGRASFVQDLLLSTL 199 (202)
Q Consensus 171 ~Ls~ee~eek~k~~~~r~eFVQgLllSTi 199 (202)
+||.||||||++ |++||||||||||
T Consensus 81 ~lS~ee~eEk~~----RseFVQ~LllSTI 105 (105)
T PF14571_consen 81 SLSDEEQEEKAQ----RSEFVQGLLLSTI 105 (105)
T ss_pred CCCHHHHHHHHH----HHHHHHHHHHhhC
Confidence 999999999986 9999999999998
No 2
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=99.79 E-value=6.1e-20 Score=125.94 Aligned_cols=54 Identities=48% Similarity=0.938 Sum_probs=52.2
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhhhhhhhccc
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHG 98 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i~Hl~~~H~ 98 (202)
++|+||||+++||+.+|+.|+.++|..+.++||||||+.+++.||++||+.+|+
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 379999999999999999999999999999999999999999999999999996
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.57 E-value=4e-08 Score=90.25 Aligned_cols=57 Identities=23% Similarity=0.549 Sum_probs=49.2
Q ss_pred ccccc-cCCCcCCCCCCCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 27 SQIDR-LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 27 s~~~~-~~~~~~~~~dd~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
-||++ +|+|-+--+++. .|+||||++ +|....+.+|+...|+.....+|||||+..+
T Consensus 61 ~dfeL~f~Ge~i~~y~~q--SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~ 119 (381)
T KOG1280|consen 61 VDFELYFGGEPISHYDPQ--SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANP 119 (381)
T ss_pred cceeeEecCccccccccc--cccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCc
Confidence 35666 677777665444 999999999 9999999999999999999999999999986
No 4
>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=95.38 E-value=0.01 Score=41.43 Aligned_cols=27 Identities=26% Similarity=0.738 Sum_probs=19.5
Q ss_pred CCceecCCCcccc--hhhhhhhhhhcccc
Q 028852 73 SKVTVCPICSVKV--ARDMLSHITLQHGH 99 (202)
Q Consensus 73 ~~~vVCPVCa~~v--s~d~i~Hl~~~H~~ 99 (202)
.....||||.+.+ ++|+-+||-+.|+.
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 4468999999987 78999999999986
No 5
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.01 E-value=0.014 Score=42.31 Aligned_cols=46 Identities=35% Similarity=0.792 Sum_probs=31.4
Q ss_pred ccCCCcCC-CCCCCCCcccCCCCCCCC--CHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 31 RLSIDDFE-VEDDVRPDFPCPYCYEDF--DIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 31 ~~~~~~~~-~~dd~~~~F~CPfC~e~~--dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
-..++|++ .+|...-+|||| ||..| ....|. ..-..+.||-|+-.+
T Consensus 6 eVeiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 6 EVEIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLII 54 (67)
T ss_pred eEEeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEE
Confidence 34577777 444567789999 88844 444443 335678999999875
No 6
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.72 E-value=0.013 Score=42.14 Aligned_cols=45 Identities=31% Similarity=0.775 Sum_probs=28.8
Q ss_pred cCCCcCCCC-CCCCCcccCCCCCC--CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 32 LSIDDFEVE-DDVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 32 ~~~~~~~~~-dd~~~~F~CPfC~e--~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
+.++|+.-+ ++..-+|+|| ||. .+.+..|. ..-..++||-|+-+|
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 334444332 2446789999 887 55555553 335678999999876
No 7
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=93.86 E-value=0.024 Score=30.99 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=14.7
Q ss_pred ccCCCCCC-CCCHHHhhhhccccc
Q 028852 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (202)
Q Consensus 47 F~CPfC~e-~~dv~~L~~H~~~eH 69 (202)
|.||+|+. --+..+|..|+...|
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 67888877 666777777766554
No 8
>PLN03086 PRLI-interacting factor K; Provisional
Probab=92.89 E-value=0.098 Score=51.50 Aligned_cols=50 Identities=22% Similarity=0.499 Sum_probs=38.8
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc-chhhhhhhhhhc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK-VARDMLSHITLQ 96 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~-vs~d~i~Hl~~~ 96 (202)
++..-+.||+|++.|....|-.|....| +.+.|| |... ...+|..|++..
T Consensus 449 el~~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~th 499 (567)
T PLN03086 449 EAKNHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQAST 499 (567)
T ss_pred ccccCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhcc
Confidence 3445679999999888999999988766 678999 9654 356888887643
No 9
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.89 E-value=0.065 Score=31.56 Aligned_cols=21 Identities=33% Similarity=0.668 Sum_probs=18.6
Q ss_pred cccCCCCCCCCCHHHhhhhcc
Q 028852 46 DFPCPYCYEDFDIASLCSHLE 66 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~ 66 (202)
..+||+|+..|....|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 578999999999999999953
No 10
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=91.90 E-value=0.099 Score=37.55 Aligned_cols=49 Identities=20% Similarity=0.517 Sum_probs=15.6
Q ss_pred cCCCCCC-CCCHHHhhhhcccccCCCCC---------------------ceecCCCcccc--hhhhhhhhhhc
Q 028852 48 PCPYCYE-DFDIASLCSHLEDEHSCESK---------------------VTVCPICSVKV--ARDMLSHITLQ 96 (202)
Q Consensus 48 ~CPfC~e-~~dv~~L~~H~~~eH~~e~~---------------------~vVCPVCa~~v--s~d~i~Hl~~~ 96 (202)
-|+||+. --++..|..|+...|.+... ...|++|.... ...+..||...
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 3999999 45688999999999987322 14599998886 56889999754
No 11
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=91.09 E-value=0.1 Score=35.78 Aligned_cols=31 Identities=26% Similarity=0.590 Sum_probs=19.9
Q ss_pred cccCCCCCC-CCCHHHhhhhcccccCCCC---CceecCCCcc
Q 028852 46 DFPCPYCYE-DFDIASLCSHLEDEHSCES---KVTVCPICSV 83 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~~H~~~eH~~e~---~~vVCPVCa~ 83 (202)
..+|||||. .+.+.. ...... ..|.|..|.+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 578999987 554433 112111 5678999977
No 12
>PHA00733 hypothetical protein
Probab=91.09 E-value=0.28 Score=39.24 Aligned_cols=51 Identities=25% Similarity=0.592 Sum_probs=37.5
Q ss_pred CcccCCCCCCC-CCHHHhhhhcccccCCCCCceecCCCcccc--hhhhhhhhhhcccc
Q 028852 45 PDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQHGH 99 (202)
Q Consensus 45 ~~F~CPfC~e~-~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v--s~d~i~Hl~~~H~~ 99 (202)
..|.|+.|+.. -....|..|... | .....|++|.... ..++..|+...|+-
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhcCc
Confidence 35999999994 456778888763 2 2346999997764 56889998877763
No 13
>PHA00732 hypothetical protein
Probab=90.98 E-value=0.24 Score=36.71 Aligned_cols=42 Identities=29% Similarity=0.652 Sum_probs=32.1
Q ss_pred ccCCCCCCC-CCHHHhhhhcccccCCCCCceecCCCcccchhhhhhhh
Q 028852 47 FPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (202)
Q Consensus 47 F~CPfC~e~-~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i~Hl 93 (202)
|.|+.|+.. -....|..|....|.. ..|++|..... ++..|+
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 789999994 4788899998765653 26999988765 466666
No 14
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.82 E-value=0.21 Score=40.47 Aligned_cols=39 Identities=18% Similarity=0.521 Sum_probs=26.9
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.....|.||.|+.-|+..+-....+ . ....+||.|...+
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEE
Confidence 3466999999999666554433322 1 3458999999876
No 15
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=90.64 E-value=0.073 Score=29.60 Aligned_cols=21 Identities=24% Similarity=0.550 Sum_probs=12.3
Q ss_pred ccCCCCCC-CCCHHHhhhhccc
Q 028852 47 FPCPYCYE-DFDIASLCSHLED 67 (202)
Q Consensus 47 F~CPfC~e-~~dv~~L~~H~~~ 67 (202)
|.||.|++ --+...|..|+..
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 56777766 4445556666543
No 16
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=90.30 E-value=0.12 Score=37.37 Aligned_cols=30 Identities=20% Similarity=0.473 Sum_probs=21.8
Q ss_pred cccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.-+||||+. .+.+. |......++|.-|.+.
T Consensus 6 lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVK---------AISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEE---------ecCceEEEEcCCCCcC
Confidence 568999999 66554 2333446999999885
No 17
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=90.28 E-value=0.11 Score=33.75 Aligned_cols=34 Identities=29% Similarity=0.657 Sum_probs=22.0
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhh
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i 90 (202)
|.||.|+... + +.+ ......||+.|...+..+.+
T Consensus 1 m~Cp~Cg~~~-~------~~D---~~~g~~vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VFD---PERGELVCPNCGLVLEENII 34 (43)
T ss_dssp ESBTTTSSSE-E------EEE---TTTTEEEETTT-BBEE-TTB
T ss_pred CCCcCCcCCc-e------EEc---CCCCeEECCCCCCEeecccc
Confidence 6899998843 2 111 44667899999888766554
No 18
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=90.00 E-value=0.28 Score=44.51 Aligned_cols=37 Identities=24% Similarity=0.600 Sum_probs=25.8
Q ss_pred CCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 44 ~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
+..|.||+|++ .+.+..|--|+... . -.-.|+||...
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH-~---l~c~C~iCGKa 196 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTH-T---LPCECGICGKA 196 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhcc-C---CCccccccccc
Confidence 66788888888 88888888887654 2 23455555554
No 19
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=89.04 E-value=0.32 Score=44.10 Aligned_cols=40 Identities=25% Similarity=0.548 Sum_probs=21.0
Q ss_pred CCcccCCCCCC-CCCHHHhhhhcccccCC--CCCceecCCCccc
Q 028852 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSC--ESKVTVCPICSVK 84 (202)
Q Consensus 44 ~~~F~CPfC~e-~~dv~~L~~H~~~eH~~--e~~~vVCPVCa~~ 84 (202)
...|.||-|++ .=+...|-.|- ..|+. +.+.-.|++|...
T Consensus 128 ~~r~~c~eCgk~ysT~snLsrHk-Q~H~~~~s~ka~~C~~C~K~ 170 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSSNLSRHK-QTHRSLDSKKAFSCKYCGKV 170 (279)
T ss_pred CCceeccccccccccccccchhh-cccccccccccccCCCCCce
Confidence 44566666666 55555566663 33332 3334456666443
No 20
>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=89.02 E-value=0.24 Score=31.08 Aligned_cols=33 Identities=18% Similarity=0.458 Sum_probs=20.8
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.+.||.|+.-|.+..-.- ......+.||.|-..
T Consensus 2 ~~~CP~C~~~~~v~~~~~------~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQL------GANGGKVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCEEEeCHHHc------CCCCCEEECCCCCCE
Confidence 368999999555443221 122347899999764
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=88.86 E-value=0.19 Score=35.04 Aligned_cols=31 Identities=19% Similarity=0.683 Sum_probs=22.6
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.|.||-|+..+.+..... .-.+.||.|.+.+
T Consensus 2 ~~~CP~CG~~iev~~~~~---------GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL---------GELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCcc---------CCEEeCCCCCCEE
Confidence 589999999776644331 3378999998863
No 22
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=88.70 E-value=0.14 Score=28.99 Aligned_cols=24 Identities=29% Similarity=0.635 Sum_probs=15.0
Q ss_pred ccCCCCCCCCCHHHhhhhcccccC
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHS 70 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~ 70 (202)
|.||+|...-....|..|+...|+
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 678888772237778888777664
No 23
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=88.61 E-value=0.22 Score=43.00 Aligned_cols=45 Identities=27% Similarity=0.732 Sum_probs=28.2
Q ss_pred CCcccCCCCCCCCC--HHHhhhhc-----ccccC--------------CCCCceecCCCcccchhh
Q 028852 44 RPDFPCPYCYEDFD--IASLCSHL-----EDEHS--------------CESKVTVCPICSVKVARD 88 (202)
Q Consensus 44 ~~~F~CPfC~e~~d--v~~L~~H~-----~~eH~--------------~e~~~vVCPVCa~~vs~d 88 (202)
...|.||.|.+.+. +...|.|. -.... ...+...||+|...++.+
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 45799999987332 44567772 22211 123456899999988553
No 24
>PLN03086 PRLI-interacting factor K; Provisional
Probab=88.20 E-value=0.38 Score=47.49 Aligned_cols=37 Identities=19% Similarity=0.491 Sum_probs=22.5
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.|.|| |+..+....|..|+. .|+- .+...|+.|...+
T Consensus 478 pv~Cp-Cg~~~~R~~L~~H~~-thCp-~Kpi~C~fC~~~v 514 (567)
T PLN03086 478 PLQCP-CGVVLEKEQMVQHQA-STCP-LRLITCRFCGDMV 514 (567)
T ss_pred CccCC-CCCCcchhHHHhhhh-ccCC-CCceeCCCCCCcc
Confidence 46677 766666667777753 3443 3556677776554
No 25
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=87.65 E-value=0.25 Score=38.38 Aligned_cols=37 Identities=19% Similarity=0.473 Sum_probs=22.6
Q ss_pred CCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchh
Q 028852 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (202)
Q Consensus 43 ~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~ 87 (202)
+...|.||+|++ ..+. +.-.+ ..-.++||+|-..-+.
T Consensus 18 lpt~f~CP~Cge-~~v~-----v~~~k--~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGK-VSIS-----VKIKK--NIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCC-eEee-----eecCC--CcceEECCCCCCccCE
Confidence 346899999995 2111 11111 2456899999886544
No 26
>PHA02768 hypothetical protein; Provisional
Probab=86.25 E-value=0.49 Score=33.23 Aligned_cols=35 Identities=26% Similarity=0.494 Sum_probs=25.5
Q ss_pred cccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.|.||.||+ =.....|..|... |. ++..|..|..-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~-H~---k~~kc~~C~k~ 40 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK-HN---TNLKLSNCKRI 40 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh-cC---CcccCCcccce
Confidence 489999999 5566789999777 44 45577777653
No 27
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.03 E-value=0.29 Score=42.14 Aligned_cols=18 Identities=28% Similarity=0.730 Sum_probs=14.2
Q ss_pred cccCCCCCCCCCHHHhhh
Q 028852 46 DFPCPYCYEDFDIASLCS 63 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~ 63 (202)
.++||+|+..|....+..
T Consensus 5 ~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRS 22 (214)
T ss_pred ceECCCCCCeeeeeEEEc
Confidence 689999999888765443
No 28
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=85.85 E-value=0.26 Score=30.97 Aligned_cols=33 Identities=21% Similarity=0.632 Sum_probs=22.8
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
..|.||-||..|++..-. .+...++||.|.+.+
T Consensus 4 Y~y~C~~Cg~~fe~~~~~--------~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKI--------SDDPLATCPECGGDV 36 (41)
T ss_pred EEEEcCCCCCEEEEEEec--------CCCCCCCCCCCCCcc
Confidence 469999999977643221 125678899998743
No 29
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=83.83 E-value=0.32 Score=38.24 Aligned_cols=36 Identities=19% Similarity=0.452 Sum_probs=23.0
Q ss_pred CCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.-+|+||||+..--++-+ -.-.....+++|-+|-..
T Consensus 20 ~k~FtCp~Cghe~vs~ct-----vkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCT-----VKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred CceEecCccCCeeeeEEE-----EEecCceeEEEcccCcce
Confidence 458999999873333222 222344567899999775
No 30
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=83.81 E-value=0.49 Score=29.36 Aligned_cols=24 Identities=29% Similarity=0.899 Sum_probs=13.0
Q ss_pred cCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcc
Q 028852 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 48 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~ 83 (202)
+||.|+.++.. .+....|||-|..
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 69999875554 5677899999974
No 31
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.04 E-value=0.56 Score=42.00 Aligned_cols=13 Identities=31% Similarity=0.920 Sum_probs=9.7
Q ss_pred CcccCCCCCCCCC
Q 028852 45 PDFPCPYCYEDFD 57 (202)
Q Consensus 45 ~~F~CPfC~e~~d 57 (202)
.++.||+|+--|-
T Consensus 18 k~ieCPvC~tkFk 30 (267)
T COG1655 18 KTIECPVCNTKFK 30 (267)
T ss_pred ceeccCcccchhh
Confidence 3799999976543
No 32
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=82.63 E-value=0.65 Score=34.70 Aligned_cols=27 Identities=30% Similarity=0.898 Sum_probs=18.3
Q ss_pred cccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcc
Q 028852 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~ 83 (202)
.|+||-||. -|+..+ +...-|||||-=
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 389999987 555432 223569999954
No 33
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=81.42 E-value=0.69 Score=28.65 Aligned_cols=24 Identities=33% Similarity=0.829 Sum_probs=15.6
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~ 83 (202)
|.|+.||.-++... ..-+||+|.+
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCC
Confidence 67888876333322 4568999976
No 34
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=80.19 E-value=1.1 Score=26.55 Aligned_cols=19 Identities=32% Similarity=0.836 Sum_probs=9.8
Q ss_pred cCCCCCCCCCHHHhhhhcc
Q 028852 48 PCPYCYEDFDIASLCSHLE 66 (202)
Q Consensus 48 ~CPfC~e~~dv~~L~~H~~ 66 (202)
.||.|++.+....+-.|++
T Consensus 3 ~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREVPENLINSHLD 21 (26)
T ss_pred cCCCCcCcccHHHHHHHHH
Confidence 4555555555555555543
No 35
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=80.02 E-value=1 Score=29.95 Aligned_cols=31 Identities=19% Similarity=0.712 Sum_probs=22.0
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcc
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~ 83 (202)
.+|.|+-|+..|++. .... +...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~---~~~~-----~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVL---QKMS-----DDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEE---EecC-----CCCCCCCCCCCC
Confidence 479999999988853 1211 145678999987
No 36
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=79.69 E-value=0.65 Score=32.15 Aligned_cols=34 Identities=26% Similarity=0.680 Sum_probs=19.6
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
+.|||||+.+++ +.+.-.. .....-=|+||-..+
T Consensus 1 i~CPyCge~~~~--~iD~s~~---~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEI--LIDPSAG---DQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEE--EEecCCC---CeeEEeehhhcCCcc
Confidence 479999997665 2222111 112234499997654
No 37
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=78.51 E-value=0.76 Score=30.18 Aligned_cols=29 Identities=17% Similarity=0.730 Sum_probs=18.7
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
+|.||-||..|++... .....||.|...+
T Consensus 3 ~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY-----------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC-----------CCceECCCCCCeE
Confidence 5888888886655211 1167888887653
No 38
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=78.24 E-value=0.93 Score=30.51 Aligned_cols=46 Identities=35% Similarity=0.690 Sum_probs=30.0
Q ss_pred CcccCCC--CCCCCCHHHhhhhcccccCCCCCceecCC----Ccccc-hhhhhhh
Q 028852 45 PDFPCPY--CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVKV-ARDMLSH 92 (202)
Q Consensus 45 ~~F~CPf--C~e~~dv~~L~~H~~~eH~~e~~~vVCPV----Ca~~v-s~d~i~H 92 (202)
....||+ |.+.+-...|-.|+..+= .-+.+.||. |..++ ..+|..|
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C--~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENEC--PKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTS--TTSEEE-SS----S--EEEHHHHHHC
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccC--CCCcEECCCCCCCCCCccchhHHhCC
Confidence 3578999 667899999999988652 346889999 98876 4455554
No 39
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.30 E-value=1.6 Score=31.14 Aligned_cols=33 Identities=30% Similarity=0.651 Sum_probs=23.6
Q ss_pred CCCcccCCCCCCC-CCHHHhhhhcccccCCCCCceecCCCc
Q 028852 43 VRPDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICS 82 (202)
Q Consensus 43 ~~~~F~CPfC~e~-~dv~~L~~H~~~eH~~e~~~vVCPVCa 82 (202)
-...|.||-||+. +-. |..|... +...+||-|-
T Consensus 22 ~~~~F~CPnCG~~~I~R---C~~CRk~----~~~Y~CP~CG 55 (59)
T PRK14890 22 KAVKFLCPNCGEVIIYR---CEKCRKQ----SNPYTCPKCG 55 (59)
T ss_pred ccCEeeCCCCCCeeEee---chhHHhc----CCceECCCCC
Confidence 3568999999994 544 4444443 6788999995
No 40
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=77.25 E-value=1.5 Score=42.05 Aligned_cols=63 Identities=21% Similarity=0.410 Sum_probs=41.1
Q ss_pred CCcCCCCCCCCCcccCCCCCC---CCCHHHhhhhcccccCCCCCceecCCCcccc-----------hhhhhhhhhhcccc
Q 028852 34 IDDFEVEDDVRPDFPCPYCYE---DFDIASLCSHLEDEHSCESKVTVCPICSVKV-----------ARDMLSHITLQHGH 99 (202)
Q Consensus 34 ~~~~~~~dd~~~~F~CPfC~e---~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v-----------s~d~i~Hl~~~H~~ 99 (202)
+++.+.++..+..|.||+|.. .+|+..|.. .+...-.|-.|-.-+ +...+++++-|-..
T Consensus 116 led~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~-------~~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~~~~Q~~p 188 (436)
T KOG2593|consen 116 LEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLD-------NETGEFHCENCGGELVEDENKLPSKESRTALNRLMEQLEP 188 (436)
T ss_pred HHHHhhhccccccccCCccccchhhhHHHHhhc-------ccCceEEEecCCCchhcccccCchHHHHHHHHHHHHHHHH
Confidence 455455556789999999987 566666655 234566788886653 33556666666666
Q ss_pred hhhh
Q 028852 100 LFKL 103 (202)
Q Consensus 100 ~~k~ 103 (202)
++..
T Consensus 189 i~d~ 192 (436)
T KOG2593|consen 189 IIDL 192 (436)
T ss_pred HHHH
Confidence 6654
No 41
>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=77.24 E-value=2 Score=28.83 Aligned_cols=33 Identities=18% Similarity=0.386 Sum_probs=20.5
Q ss_pred ccCCCCCC------------CCCHHHhhhhcccccCCCCCceecCCCcccch
Q 028852 47 FPCPYCYE------------DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (202)
Q Consensus 47 F~CPfC~e------------~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs 86 (202)
|.||.|++ -|+...+..++.. ...||+|...++
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~~-------~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQTYERRAIEKWLLS-------HGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCEEeHHHHHHHHHH-------CCCCCCCcCCCC
Confidence 56666654 3555555555543 468999987663
No 42
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=77.12 E-value=1.2 Score=43.20 Aligned_cols=34 Identities=32% Similarity=0.692 Sum_probs=29.4
Q ss_pred CCCCCcccCCCCCCCC-CHHHhhhhcccccCCCCC
Q 028852 41 DDVRPDFPCPYCYEDF-DIASLCSHLEDEHSCESK 74 (202)
Q Consensus 41 dd~~~~F~CPfC~e~~-dv~~L~~H~~~eH~~e~~ 74 (202)
++.+.-|.||+|.++| +...|-+|++.+|..+..
T Consensus 10 ~~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ed~ 44 (505)
T KOG1842|consen 10 GEILEGFLCPICLLDLPNLSALNDHLDVEHFEEDE 44 (505)
T ss_pred chhhhcccCchHhhhhhhHHHHHHHHhhhccccch
Confidence 4677889999999976 578899999999999775
No 43
>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=76.74 E-value=1.1 Score=33.48 Aligned_cols=34 Identities=21% Similarity=0.615 Sum_probs=15.1
Q ss_pred CCcccCCCCC-C-CCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 44 RPDFPCPYCY-E-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 44 ~~~F~CPfC~-e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
...|.||||+ + .+.+ .-+-......+.|-+|...
T Consensus 20 ~~~F~CPfC~~~~sV~v-------~idkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSV-------KIDKKEGIGILSCRVCGES 55 (81)
T ss_dssp SS----TTT--SS-EEE-------EEETTTTEEEEEESSS--E
T ss_pred CceEcCCcCCCCCeEEE-------EEEccCCEEEEEecCCCCe
Confidence 4589999998 4 3322 1122244557889999665
No 44
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=76.10 E-value=0.73 Score=47.11 Aligned_cols=52 Identities=25% Similarity=0.498 Sum_probs=40.9
Q ss_pred CCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc--hhhhhhhhhh
Q 028852 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITL 95 (202)
Q Consensus 44 ~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v--s~d~i~Hl~~ 95 (202)
.+..+||||+. .--+..|..|+.-.|--..-+.-|+.|.... ...+-+|+.+
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~~ 262 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQL 262 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHHh
Confidence 35689999999 6678899999999999888888899998875 2345555543
No 45
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=76.02 E-value=1 Score=32.16 Aligned_cols=26 Identities=35% Similarity=0.884 Sum_probs=20.9
Q ss_pred CcccCCCCCCCC-CHHHhhhhcccccC
Q 028852 45 PDFPCPYCYEDF-DIASLCSHLEDEHS 70 (202)
Q Consensus 45 ~~F~CPfC~e~~-dv~~L~~H~~~eH~ 70 (202)
..|.|++|+..| +...|..|+...+-
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 89999999997643
No 46
>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=74.43 E-value=1.9 Score=28.91 Aligned_cols=9 Identities=22% Similarity=0.490 Sum_probs=4.5
Q ss_pred CCHHHhhhh
Q 028852 56 FDIASLCSH 64 (202)
Q Consensus 56 ~dv~~L~~H 64 (202)
+...+|..|
T Consensus 12 Y~~~~LlqH 20 (43)
T PF03470_consen 12 YKYRELLQH 20 (43)
T ss_pred eehhHHHHH
Confidence 445555554
No 47
>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=74.35 E-value=1.4 Score=27.67 Aligned_cols=26 Identities=27% Similarity=0.599 Sum_probs=16.8
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.|.|+.||.-++-.. ..-+||||.+.
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 478999987433211 23599999874
No 48
>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=74.34 E-value=1.6 Score=24.95 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=15.7
Q ss_pred ccCCCCCC-CCCHHHhhhhccccc
Q 028852 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (202)
Q Consensus 47 F~CPfC~e-~~dv~~L~~H~~~eH 69 (202)
|.|..|++ --+...|..|....|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 67778877 556777777765444
No 49
>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=73.18 E-value=1.7 Score=36.27 Aligned_cols=54 Identities=28% Similarity=0.611 Sum_probs=32.8
Q ss_pred CcccCCC----CCCCCCHHHhhhhcccccCCCCCceecCC----Cccc-chhhhhhhhhhcccchh
Q 028852 45 PDFPCPY----CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVK-VARDMLSHITLQHGHLF 101 (202)
Q Consensus 45 ~~F~CPf----C~e~~dv~~L~~H~~~eH~~e~~~vVCPV----Ca~~-vs~d~i~Hl~~~H~~~~ 101 (202)
-.|+||| |.+.+-......| +++-. -++..||+ |.-. ...++..|+...|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~H-E~~C~--~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREH-EEECP--FRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHH-HHT-T--TSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhH-hccCC--CcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 3799999 9998888888899 34433 45678999 6433 35689999999999843
No 50
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=72.20 E-value=3.4 Score=29.70 Aligned_cols=34 Identities=29% Similarity=0.742 Sum_probs=22.2
Q ss_pred CCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCc
Q 028852 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICS 82 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa 82 (202)
|-...|+||-||+ .+-.-.-|.- -.+..+||-|-
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 4456899999997 5544333321 25677899884
No 51
>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=71.94 E-value=3.6 Score=29.37 Aligned_cols=38 Identities=18% Similarity=0.357 Sum_probs=22.9
Q ss_pred CCcccCCCCCC------------CCCHHHhhhhcccccCCCCCceecCCCcccchh
Q 028852 44 RPDFPCPYCYE------------DFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (202)
Q Consensus 44 ~~~F~CPfC~e------------~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~ 87 (202)
+..|.||.|++ -|+...+..++.. ...+||+|...++.
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLSE 51 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-SG
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCCc
Confidence 45789999865 3555666666544 57899999776643
No 52
>PRK12495 hypothetical protein; Provisional
Probab=71.82 E-value=2.5 Score=37.44 Aligned_cols=31 Identities=19% Similarity=0.433 Sum_probs=23.4
Q ss_pred CCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchh
Q 028852 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~ 87 (202)
...|.||.||..+- .+ ...++||+|-..+..
T Consensus 40 msa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGDPIF------------RH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccCccc------------CC-CCeeECCCCCCcccc
Confidence 34799999999554 22 567899999988743
No 53
>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=71.81 E-value=2.1 Score=25.35 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=9.8
Q ss_pred CCCcccCCCCCC
Q 028852 43 VRPDFPCPYCYE 54 (202)
Q Consensus 43 ~~~~F~CPfC~e 54 (202)
....|+||-||+
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 356899999986
No 54
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=71.56 E-value=3 Score=35.16 Aligned_cols=33 Identities=24% Similarity=0.429 Sum_probs=24.0
Q ss_pred CCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 43 ~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
....|.||-|+.-|+..+-.. ..-.||+|-..+
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCC
Confidence 356899999999555544332 367999999876
No 55
>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=70.77 E-value=1.9 Score=29.26 Aligned_cols=33 Identities=24% Similarity=0.546 Sum_probs=17.2
Q ss_pred ccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 47 FPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 47 F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
-+|||||- +.-+.. .+ .-........|+-|-+.
T Consensus 2 kPCPfCGg~~~~~~~--~~---~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 2 KPCPFCGGADVYLRR--GF---DPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCcceeeEe--cc---CCCCCEEEEECCCCCCC
Confidence 48999987 442210 01 00112223479999775
No 56
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=70.47 E-value=1.3 Score=33.99 Aligned_cols=32 Identities=19% Similarity=0.508 Sum_probs=21.8
Q ss_pred CCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.+...|.||||+. .+...+ ..-..|--|-..+
T Consensus 32 ~q~a~y~CpfCgk~~vkR~a------------~GIW~C~~C~~~~ 64 (90)
T PTZ00255 32 SQHAKYFCPFCGKHAVKRQA------------VGIWRCKGCKKTV 64 (90)
T ss_pred HHhCCccCCCCCCCceeeee------------eEEEEcCCCCCEE
Confidence 6778999999987 554322 2345677777665
No 57
>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=69.99 E-value=3.4 Score=34.03 Aligned_cols=34 Identities=21% Similarity=0.377 Sum_probs=25.3
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.....|.||-|+.-++..+-.. ..-.||+|...+
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 3456899999998666555554 267999999875
No 58
>smart00355 ZnF_C2H2 zinc finger.
Probab=69.72 E-value=3.4 Score=22.15 Aligned_cols=20 Identities=25% Similarity=0.546 Sum_probs=12.6
Q ss_pred ccCCCCCC-CCCHHHhhhhcc
Q 028852 47 FPCPYCYE-DFDIASLCSHLE 66 (202)
Q Consensus 47 F~CPfC~e-~~dv~~L~~H~~ 66 (202)
|.|+.|+. --....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 56777777 445556666655
No 59
>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=69.24 E-value=2.8 Score=40.64 Aligned_cols=42 Identities=31% Similarity=0.351 Sum_probs=32.4
Q ss_pred CCCcccCCCCCC-CCCHHHhhhhcccccCCCCCc---eecCCCccc
Q 028852 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKV---TVCPICSVK 84 (202)
Q Consensus 43 ~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~---vVCPVCa~~ 84 (202)
-+.--.||+|.+ -.|..++..|+..+|...-.+ -+.|-+...
T Consensus 54 sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~ 99 (466)
T PF04780_consen 54 SWRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDD 99 (466)
T ss_pred ceeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCH
Confidence 355678999999 999999999999999986543 355654443
No 60
>PHA00616 hypothetical protein
Probab=69.13 E-value=2 Score=28.95 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=17.4
Q ss_pred ccCCCCCC-CCCHHHhhhhcccccCC
Q 028852 47 FPCPYCYE-DFDIASLCSHLEDEHSC 71 (202)
Q Consensus 47 F~CPfC~e-~~dv~~L~~H~~~eH~~ 71 (202)
|.||.||. =....+|..|+...|.-
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 67777777 55667777777666654
No 61
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=68.74 E-value=2.6 Score=36.27 Aligned_cols=44 Identities=20% Similarity=0.597 Sum_probs=27.2
Q ss_pred CCcccCCCCCCCCCHH----HhhhhcccccCC---CCCceecCCCcccchh
Q 028852 44 RPDFPCPYCYEDFDIA----SLCSHLEDEHSC---ESKVTVCPICSVKVAR 87 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~----~L~~H~~~eH~~---e~~~vVCPVCa~~vs~ 87 (202)
...|.||.|-..+... .=|-|+-=.-+. -.+.++||+|-.++..
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 3579999996644433 345554322222 2356889999987754
No 62
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=67.87 E-value=4.2 Score=25.79 Aligned_cols=31 Identities=26% Similarity=0.643 Sum_probs=20.5
Q ss_pred cccCCCCCCCCCHH--HhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIA--SLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~--~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
...||-|+..|.+. .|- ...+.|.||-|...
T Consensus 2 ~i~CP~C~~~f~v~~~~l~--------~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLP--------AGGRKVRCPKCGHV 34 (37)
T ss_pred EEECCCCCceEEcCHHHcc--------cCCcEEECCCCCcE
Confidence 35799998855443 332 23668899999753
No 63
>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=66.83 E-value=1.2 Score=25.94 Aligned_cols=11 Identities=45% Similarity=1.419 Sum_probs=9.1
Q ss_pred cccCCCCCCCC
Q 028852 46 DFPCPYCYEDF 56 (202)
Q Consensus 46 ~F~CPfC~e~~ 56 (202)
-|.||+|+..|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 49999998755
No 64
>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=66.63 E-value=0.67 Score=34.10 Aligned_cols=54 Identities=24% Similarity=0.405 Sum_probs=25.7
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc-------hhhhhhhhhhcccchhhhh
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV-------ARDMLSHITLQHGHLFKLQ 104 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v-------s~d~i~Hl~~~H~~~~k~~ 104 (202)
..||-|...++..+-.-||..=+..=...+.||-|...+ ..|+.- +|++.++.|
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC----~~c~gLiSK 62 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFC----NHCHGLISK 62 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-T
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceee----ccCCceeec
Confidence 467888777776663333332222224568899998875 246554 577777543
No 65
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=66.02 E-value=1.7 Score=28.32 Aligned_cols=31 Identities=23% Similarity=0.642 Sum_probs=22.0
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcc
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~ 83 (202)
.+|.|+-||..|++-.-. .+...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~~--------~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSI--------SEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEc--------CCCCCCcCCCCCC
Confidence 469999999877653211 2256789999987
No 66
>PF15616 TerY-C: TerY-C metal binding domain
Probab=65.56 E-value=2.8 Score=34.21 Aligned_cols=42 Identities=19% Similarity=0.404 Sum_probs=29.8
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCC-CCCceecCCCcccchhhh
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSC-ESKVTVCPICSVKVARDM 89 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~-e~~~vVCPVCa~~vs~d~ 89 (202)
.=.||+||..+-++- | =|-.-|++ +...++||-|-....-..
T Consensus 77 ~PgCP~CGn~~~fa~-C-~CGkl~Ci~g~~~~~CPwCg~~g~~~~ 119 (131)
T PF15616_consen 77 APGCPHCGNQYAFAV-C-GCGKLFCIDGEGEVTCPWCGNEGSFGA 119 (131)
T ss_pred CCCCCCCcChhcEEE-e-cCCCEEEeCCCCCEECCCCCCeeeecc
Confidence 468999998544432 2 47788884 566899999988764433
No 67
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=65.02 E-value=3.8 Score=27.22 Aligned_cols=28 Identities=21% Similarity=0.553 Sum_probs=21.5
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.|.|.-||.+|++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58899999977754 34578999998765
No 68
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=64.68 E-value=3 Score=38.99 Aligned_cols=58 Identities=29% Similarity=0.559 Sum_probs=38.1
Q ss_pred cccCCCCCCCCCHHHh---hhhcccccCCCCC-ceecCCCcccc--------------------------hhhhhhhhhh
Q 028852 46 DFPCPYCYEDFDIASL---CSHLEDEHSCESK-VTVCPICSVKV--------------------------ARDMLSHITL 95 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L---~~H~~~eH~~e~~-~vVCPVCa~~v--------------------------s~d~i~Hl~~ 95 (202)
.-.|--|+.-+-|-+= |+|+-=.-+.-+. -.+||.|..+| .+||..||++
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 5677777776555543 4443322222111 46899999885 3699999999
Q ss_pred cccchhhh
Q 028852 96 QHGHLFKL 103 (202)
Q Consensus 96 ~H~~~~k~ 103 (202)
+|+...+-
T Consensus 170 rH~~~~~p 177 (389)
T KOG2932|consen 170 RHGSLLQP 177 (389)
T ss_pred hhccccCC
Confidence 99987654
No 69
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=64.54 E-value=1.9 Score=33.26 Aligned_cols=32 Identities=19% Similarity=0.644 Sum_probs=21.2
Q ss_pred CCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.+...|+||||+. .+... ...-..|--|-..+
T Consensus 31 ~q~a~y~CpfCgk~~vkR~------------a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 31 QQKAKYVCPFCGKKTVKRG------------STGIWTCRKCGAKF 63 (91)
T ss_pred HHhcCccCCCCCCCceEEE------------eeEEEEcCCCCCEE
Confidence 5678999999987 44332 23345577776665
No 70
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=64.51 E-value=5.9 Score=33.91 Aligned_cols=45 Identities=20% Similarity=0.350 Sum_probs=30.6
Q ss_pred CCCcCCCCCCCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhhhhh
Q 028852 33 SIDDFEVEDDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (202)
Q Consensus 33 ~~~~~~~~dd~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i~Hl 93 (202)
|+..+..+++....=.||.||. ...+...||.|....-+|..+=+
T Consensus 296 ~~~~v~~~~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~ 340 (364)
T COG0675 296 GGIVVKVVPPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAAL 340 (364)
T ss_pred CCeEEEECCCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHH
Confidence 4444444444556688999998 33678899999987766665433
No 71
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=64.47 E-value=3.9 Score=27.57 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=19.8
Q ss_pred cccCCCCCCCCCHHHhhhhcccccC
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHS 70 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~ 70 (202)
.+.||.|...+.. .|..|+...|.
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 89999988774
No 72
>PF12773 DZR: Double zinc ribbon
Probab=64.39 E-value=4.5 Score=26.44 Aligned_cols=29 Identities=21% Similarity=0.540 Sum_probs=19.1
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccch
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs 86 (202)
.-.||.||..+. ..+...++||.|.+.+.
T Consensus 12 ~~fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 12 AKFCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred ccCChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 345777776555 34556788999987653
No 73
>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=63.28 E-value=9.3 Score=26.51 Aligned_cols=47 Identities=26% Similarity=0.522 Sum_probs=31.6
Q ss_pred CCCcCCCCCCCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhhh
Q 028852 33 SIDDFEVEDDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLS 91 (202)
Q Consensus 33 ~~~~~~~~dd~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i~ 91 (202)
|+.-++++ +.-.+=.||.||.-... ....+..+||.|-....+|+.+
T Consensus 16 G~~v~~v~-~~~TSq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~rD~na 62 (69)
T PF07282_consen 16 GIQVVEVD-EAYTSQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMDRDVNA 62 (69)
T ss_pred CCEEEEEC-CCCCccCccCccccccc-----------ccccceEEcCCCCCEECcHHHH
Confidence 44444443 34477889999882222 4556789999999888777655
No 74
>PRK00420 hypothetical protein; Validated
Probab=63.20 E-value=5.3 Score=31.71 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=19.3
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.-.||.||-.+-. .....++||+|...+
T Consensus 23 ~~~CP~Cg~pLf~------------lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLFE------------LKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCccee------------cCCCceECCCCCCee
Confidence 3689999863311 124578999998864
No 75
>PF14353 CpXC: CpXC protein
Probab=62.43 E-value=3.1 Score=32.41 Aligned_cols=37 Identities=27% Similarity=0.590 Sum_probs=21.4
Q ss_pred ccCCCCCCCC--CHHHhhhhcccccC--------CCCCceecCCCcccc
Q 028852 47 FPCPYCYEDF--DIASLCSHLEDEHS--------CESKVTVCPICSVKV 85 (202)
Q Consensus 47 F~CPfC~e~~--dv~~L~~H~~~eH~--------~e~~~vVCPVCa~~v 85 (202)
.+||.|+..| ++-.++.= +..+ .+-...+||-|....
T Consensus 2 itCP~C~~~~~~~v~~~I~~--~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINA--DEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcC--cCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 5899998844 33333221 1221 244568899998864
No 76
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=62.20 E-value=2.3 Score=32.72 Aligned_cols=32 Identities=22% Similarity=0.537 Sum_probs=20.7
Q ss_pred CCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.+...|+||||+. .+-.. ...-..|.-|-..+
T Consensus 32 ~q~a~y~CpfCgk~~vkR~------------a~GIW~C~~C~~~~ 64 (90)
T PRK03976 32 KMRAKHVCPVCGRPKVKRV------------GTGIWECRKCGAKF 64 (90)
T ss_pred HHhcCccCCCCCCCceEEE------------EEEEEEcCCCCCEE
Confidence 5678999999977 54432 12334577776655
No 77
>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=61.82 E-value=2.7 Score=32.95 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=22.6
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
+.+..+.|+-|+..|.+... ...||-|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 45678999999987766533 4679999864
No 78
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=61.30 E-value=3.5 Score=39.09 Aligned_cols=35 Identities=31% Similarity=0.747 Sum_probs=20.3
Q ss_pred CCCCCCCCCHHH-----------hhhhcccccCCCCCceecCCCccc
Q 028852 49 CPYCYEDFDIAS-----------LCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 49 CPfC~e~~dv~~-----------L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
||.|-|.+|+.. +|..|- .|--+.-++.||-|.-+
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 777766666542 222221 12223468999999876
No 79
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=60.49 E-value=5.3 Score=33.76 Aligned_cols=25 Identities=36% Similarity=0.822 Sum_probs=18.1
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.+.||.||-- |.. -.+.+||||-+.
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 112 457899999874
No 80
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=59.93 E-value=4.7 Score=37.91 Aligned_cols=40 Identities=23% Similarity=0.517 Sum_probs=31.5
Q ss_pred cccCCC--CCC-CCCHHHhhhhcccccCC-----------------CCCceecCCCcccc
Q 028852 46 DFPCPY--CYE-DFDIASLCSHLEDEHSC-----------------ESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPf--C~e-~~dv~~L~~H~~~eH~~-----------------e~~~vVCPVCa~~v 85 (202)
-|+||. |.+ .-+.-+|--|...-|+. +.++.+|+||..+-
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhh
Confidence 489986 888 77888999988888832 44678999999864
No 81
>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=59.82 E-value=5.5 Score=31.13 Aligned_cols=38 Identities=26% Similarity=0.596 Sum_probs=22.1
Q ss_pred ccCCCCCCCCCH---HHhhhhcccccCCCCCceecCCCcccchh
Q 028852 47 FPCPYCYEDFDI---ASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (202)
Q Consensus 47 F~CPfC~e~~dv---~~L~~H~~~eH~~e~~~vVCPVCa~~vs~ 87 (202)
-.|||||....+ ..+.-|-.+.+ ...-+|+-|-+.||.
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~---~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDG---PYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCC---ceeEECCCCCceeee
Confidence 469999883332 22222222221 223799999999854
No 82
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=59.82 E-value=4.9 Score=32.84 Aligned_cols=26 Identities=23% Similarity=0.691 Sum_probs=18.6
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
...||-||--+ ..| ...|+||||-..
T Consensus 28 ~~hCp~Cg~PL-----F~K--------dG~v~CPvC~~~ 53 (131)
T COG1645 28 AKHCPKCGTPL-----FRK--------DGEVFCPVCGYR 53 (131)
T ss_pred HhhCcccCCcc-----eee--------CCeEECCCCCce
Confidence 47899998732 122 457999999854
No 83
>PRK12496 hypothetical protein; Provisional
Probab=59.34 E-value=6.5 Score=32.64 Aligned_cols=28 Identities=25% Similarity=0.481 Sum_probs=19.7
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccch
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs 86 (202)
.|.||.|+..|+.. ...-+||||...+.
T Consensus 127 ~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPED-------------YPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCC-------------CCCCcCCCCCChhh
Confidence 48899999876531 22358999988653
No 84
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=58.75 E-value=4.4 Score=31.60 Aligned_cols=9 Identities=67% Similarity=1.575 Sum_probs=7.6
Q ss_pred cccCCCCCC
Q 028852 46 DFPCPYCYE 54 (202)
Q Consensus 46 ~F~CPfC~e 54 (202)
-++|||||+
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 478999998
No 85
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=58.68 E-value=6.1 Score=23.58 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=4.1
Q ss_pred CCCCCCCC
Q 028852 49 CPYCYEDF 56 (202)
Q Consensus 49 CPfC~e~~ 56 (202)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 55555543
No 86
>PF13395 HNH_4: HNH endonuclease
Probab=57.65 E-value=5.9 Score=26.82 Aligned_cols=14 Identities=43% Similarity=1.058 Sum_probs=12.1
Q ss_pred CCCCCCCCCHHHhh
Q 028852 49 CPYCYEDFDIASLC 62 (202)
Q Consensus 49 CPfC~e~~dv~~L~ 62 (202)
|||||+.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999988763
No 87
>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=57.53 E-value=2.7 Score=35.34 Aligned_cols=40 Identities=25% Similarity=0.613 Sum_probs=20.8
Q ss_pred CCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
+-.|+||.|+..+...++.. ...-........||-|....
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B-
T ss_pred ceEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcC
Confidence 35799999999887777655 11112235568899998874
No 88
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=57.02 E-value=4.6 Score=28.99 Aligned_cols=27 Identities=33% Similarity=0.799 Sum_probs=22.3
Q ss_pred ceecCCCcccc--hhhhhhhhhhcccchh
Q 028852 75 VTVCPICSVKV--ARDMLSHITLQHGHLF 101 (202)
Q Consensus 75 ~vVCPVCa~~v--s~d~i~Hl~~~H~~~~ 101 (202)
...||-|.+.. ..+.++|++-.|++.|
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~~~~ 45 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHGWLF 45 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhhhhh
Confidence 45688887765 6799999999999987
No 89
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=56.95 E-value=9.6 Score=26.47 Aligned_cols=33 Identities=15% Similarity=0.431 Sum_probs=15.8
Q ss_pred CCCcccCCCCCCC-------------CCHHHhhhhcccccCCCCCceecCC
Q 028852 43 VRPDFPCPYCYED-------------FDIASLCSHLEDEHSCESKVTVCPI 80 (202)
Q Consensus 43 ~~~~F~CPfC~e~-------------~dv~~L~~H~~~eH~~e~~~vVCPV 80 (202)
....|.||+.... |+...+..++ ...+.+.|||
T Consensus 8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv 53 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPV 53 (57)
T ss_dssp SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHC-----TTTS-EE-SC
T ss_pred cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCC
Confidence 3456778776543 4444444444 2456788888
No 90
>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=56.82 E-value=9.1 Score=30.05 Aligned_cols=33 Identities=24% Similarity=0.666 Sum_probs=24.0
Q ss_pred CCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccchh
Q 028852 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~ 87 (202)
++-....||-||. -+|+ ...++|||-|.+..-.
T Consensus 5 elGtKR~Cp~CG~kFYDL-------------nk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDL-------------NKDPIVCPKCGTEFPP 38 (108)
T ss_pred ccCCcccCCCCcchhccC-------------CCCCccCCCCCCccCc
Confidence 4556789999998 4443 2468999999886543
No 91
>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=55.82 E-value=4.3 Score=25.68 Aligned_cols=18 Identities=33% Similarity=0.715 Sum_probs=7.5
Q ss_pred eecCCCcccc-hhhhhhhh
Q 028852 76 TVCPICSVKV-ARDMLSHI 93 (202)
Q Consensus 76 vVCPVCa~~v-s~d~i~Hl 93 (202)
+.||.|.-.+ ..-|..||
T Consensus 5 ~~C~nC~R~v~a~RfA~HL 23 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAPHL 23 (33)
T ss_dssp EE-TTTSSEEEGGGHHHHH
T ss_pred EECCCCcCCcchhhhHHHH
Confidence 3455554443 22344444
No 92
>smart00507 HNHc HNH nucleases.
Probab=55.10 E-value=3.8 Score=25.50 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=13.8
Q ss_pred ccCCCCCCCCCHHHhhhhccc
Q 028852 47 FPCPYCYEDFDIASLCSHLED 67 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~ 67 (202)
+.|+||+..++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 799999996654334455554
No 93
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=54.89 E-value=9.1 Score=26.83 Aligned_cols=27 Identities=30% Similarity=0.778 Sum_probs=18.8
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.-.||.|++.|.. +.-.||||.|.+.-
T Consensus 5 ~~~C~~Cg~~~~~-------------~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKD-------------GDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccC-------------CCCEEECCCCCCcc
Confidence 3579999886631 23468999998753
No 94
>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=52.43 E-value=9.8 Score=32.95 Aligned_cols=36 Identities=31% Similarity=0.572 Sum_probs=20.7
Q ss_pred CCCCCC--CCCHHHhhhhcccccCC------CCCceecCCCccc
Q 028852 49 CPYCYE--DFDIASLCSHLEDEHSC------ESKVTVCPICSVK 84 (202)
Q Consensus 49 CPfC~e--~~dv~~L~~H~~~eH~~------e~~~vVCPVCa~~ 84 (202)
||.||. +-.+.+||.=|--+... .....+||.|-+.
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 677776 33334666555433221 2356789999873
No 95
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=52.37 E-value=5 Score=31.34 Aligned_cols=30 Identities=20% Similarity=0.331 Sum_probs=21.3
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
+.+..+.|+-|+..|.+.. ....||-|-..
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 4577899999997655433 33469999864
No 96
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.22 E-value=6 Score=31.86 Aligned_cols=43 Identities=16% Similarity=0.443 Sum_probs=24.2
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcc-----cccCC---CCCceecCCCccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLE-----DEHSC---ESKVTVCPICSVK 84 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~-----~eH~~---e~~~vVCPVCa~~ 84 (202)
..+..+.|+-||..+.+..--.++. .-|-. ......||-|-..
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 4567899999998665542111111 11111 1344679999764
No 97
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=51.85 E-value=6.1 Score=22.81 Aligned_cols=6 Identities=50% Similarity=1.398 Sum_probs=3.2
Q ss_pred CCCCCC
Q 028852 49 CPYCYE 54 (202)
Q Consensus 49 CPfC~e 54 (202)
||.||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 555554
No 98
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=51.82 E-value=8.2 Score=36.75 Aligned_cols=55 Identities=25% Similarity=0.431 Sum_probs=42.2
Q ss_pred CCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCccc--------------------------------------
Q 028852 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK-------------------------------------- 84 (202)
Q Consensus 44 ~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~-------------------------------------- 84 (202)
.--=.|-||.. =+|-.+|..||...|- .|-||..+
T Consensus 218 KGHP~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf 291 (493)
T COG5236 218 KGHPLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVF 291 (493)
T ss_pred CCCchhhhccceecChHHHHHHHHhhhh------hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEe
Confidence 34567999999 8899999999999885 35555433
Q ss_pred c-hhhhhhhhhhcccchhhhh
Q 028852 85 V-ARDMLSHITLQHGHLFKLQ 104 (202)
Q Consensus 85 v-s~d~i~Hl~~~H~~~~k~~ 104 (202)
+ -..++.||+..||...|.+
T Consensus 292 ~~~~el~~h~~~~h~~~~~~~ 312 (493)
T COG5236 292 PYHTELLEHLTRFHKVNARLS 312 (493)
T ss_pred ccHHHHHHHHHHHhhcccccC
Confidence 1 2468999999999988664
No 99
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=50.89 E-value=6.1 Score=34.32 Aligned_cols=26 Identities=15% Similarity=0.470 Sum_probs=16.8
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCC
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSC 71 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~ 71 (202)
.|.||.|+..+.+..=-=+|...|.+
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~f 27 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQF 27 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCC
Confidence 48999999966433222345667777
No 100
>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=50.14 E-value=8.5 Score=26.30 Aligned_cols=14 Identities=36% Similarity=0.942 Sum_probs=11.7
Q ss_pred CCCCCcccCCCCCC
Q 028852 41 DDVRPDFPCPYCYE 54 (202)
Q Consensus 41 dd~~~~F~CPfC~e 54 (202)
+++...|.||.|+.
T Consensus 29 ~~Lp~~w~CP~C~a 42 (50)
T cd00730 29 EDLPDDWVCPVCGA 42 (50)
T ss_pred hHCCCCCCCCCCCC
Confidence 35788999999986
No 101
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.77 E-value=11 Score=22.11 Aligned_cols=9 Identities=33% Similarity=0.951 Sum_probs=5.9
Q ss_pred ccCCCCCCC
Q 028852 47 FPCPYCYED 55 (202)
Q Consensus 47 F~CPfC~e~ 55 (202)
-.||.||..
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 357777763
No 102
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=49.56 E-value=6.4 Score=30.25 Aligned_cols=32 Identities=19% Similarity=0.604 Sum_probs=19.4
Q ss_pred CCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.+...|.||||+. .+... ...--.|.-|-..+
T Consensus 31 ~q~~ky~Cp~Cgk~~vkR~------------a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 31 SQHAKYTCPFCGKTSVKRV------------ATGIWKCKKCGKKF 63 (90)
T ss_dssp HHHS-BEESSSSSSEEEEE------------ETTEEEETTTTEEE
T ss_pred HHhCCCcCCCCCCceeEEe------------eeEEeecCCCCCEE
Confidence 4567899999998 44322 22334577776654
No 103
>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=49.30 E-value=8.9 Score=30.50 Aligned_cols=25 Identities=28% Similarity=0.946 Sum_probs=16.3
Q ss_pred cCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 48 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
+||-|+-++.- -+....|||-|+.-
T Consensus 4 ~CP~C~seytY------------~dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTY------------HDGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceE------------ecCCeeECcccccc
Confidence 68888654321 14557899999764
No 104
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=49.12 E-value=13 Score=21.44 Aligned_cols=20 Identities=25% Similarity=0.404 Sum_probs=12.9
Q ss_pred ccCCCCCC-CCCHHHhhhhcc
Q 028852 47 FPCPYCYE-DFDIASLCSHLE 66 (202)
Q Consensus 47 F~CPfC~e-~~dv~~L~~H~~ 66 (202)
|.|+.|+. =-+...+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 66777777 445666666654
No 105
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=49.02 E-value=14 Score=23.36 Aligned_cols=31 Identities=19% Similarity=0.548 Sum_probs=19.0
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~ 83 (202)
+.||-|+.-|++.+-. =+.....|.||.|..
T Consensus 3 i~Cp~C~~~y~i~d~~------ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK------IPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHHH------CCCCCcEEECCCCCC
Confidence 5788888844443321 123456788888865
No 106
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=48.48 E-value=9.3 Score=35.27 Aligned_cols=39 Identities=26% Similarity=0.479 Sum_probs=23.5
Q ss_pred cccCCCCCC--CCCHH----------HhhhhcccccCCCCCceecCCCcccc
Q 028852 46 DFPCPYCYE--DFDIA----------SLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e--~~dv~----------~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.+.||.|-. .++-. .+|..|.+..- ......||+|-..+
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~-~~~~~~CP~C~~~l 53 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLF-VRGSGSCPECDTPL 53 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHh-cCCCCCCCCCCCcc
Confidence 378999965 22221 23445555542 33457899998765
No 107
>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=48.07 E-value=8.7 Score=25.96 Aligned_cols=14 Identities=36% Similarity=0.942 Sum_probs=8.8
Q ss_pred CCCCCcccCCCCCC
Q 028852 41 DDVRPDFPCPYCYE 54 (202)
Q Consensus 41 dd~~~~F~CPfC~e 54 (202)
++++..|.||.|+.
T Consensus 29 ~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 29 EDLPDDWVCPVCGA 42 (47)
T ss_dssp GGS-TT-B-TTTSS
T ss_pred HHCCCCCcCcCCCC
Confidence 46778999999976
No 108
>PRK03922 hypothetical protein; Provisional
Probab=47.61 E-value=9.2 Score=30.57 Aligned_cols=14 Identities=50% Similarity=0.736 Sum_probs=11.7
Q ss_pred cccCCCCCCCCCHH
Q 028852 46 DFPCPYCYEDFDIA 59 (202)
Q Consensus 46 ~F~CPfC~e~~dv~ 59 (202)
.-.||+|++.|+-+
T Consensus 49 ~~~cP~cge~~~~a 62 (113)
T PRK03922 49 LTICPKCGEPFDSA 62 (113)
T ss_pred cccCCCCCCcCCcE
Confidence 67899999998754
No 109
>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=47.31 E-value=8.2 Score=27.78 Aligned_cols=14 Identities=29% Similarity=0.933 Sum_probs=9.7
Q ss_pred CCCCceecCCCccc
Q 028852 71 CESKVTVCPICSVK 84 (202)
Q Consensus 71 ~e~~~vVCPVCa~~ 84 (202)
+....-+||+|.-.
T Consensus 47 ~~~~~~iCp~C~~i 60 (69)
T PF09706_consen 47 FNNDADICPICELI 60 (69)
T ss_pred CcCCCccCHHHHHH
Confidence 34456789999754
No 110
>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=46.98 E-value=6.3 Score=30.16 Aligned_cols=38 Identities=29% Similarity=0.679 Sum_probs=12.5
Q ss_pred cCCCCCCCCCHHHhh-hhcccccCC-----------CCCceecCCCcccc
Q 028852 48 PCPYCYEDFDIASLC-SHLEDEHSC-----------ESKVTVCPICSVKV 85 (202)
Q Consensus 48 ~CPfC~e~~dv~~L~-~H~~~eH~~-----------e~~~vVCPVCa~~v 85 (202)
.||+|++.+...++. .=|..-|.+ +...-+|++|..+.
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 699999977665543 447777765 55568899998764
No 111
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=46.72 E-value=11 Score=24.17 Aligned_cols=10 Identities=50% Similarity=1.175 Sum_probs=7.5
Q ss_pred CCceecCCCc
Q 028852 73 SKVTVCPICS 82 (202)
Q Consensus 73 ~~~vVCPVCa 82 (202)
...++||||-
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 5578888884
No 112
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=46.52 E-value=9.3 Score=30.24 Aligned_cols=37 Identities=24% Similarity=0.629 Sum_probs=21.2
Q ss_pred CCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
...|.||||.-.= ..-+-++..|. ....-|-||..-.
T Consensus 21 dt~FnClfcnHek---~v~~~~Dk~~~--iG~~sC~iC~esF 57 (109)
T KOG3214|consen 21 DTQFNCLFCNHEK---SVSCTLDKKHN--IGKASCRICEESF 57 (109)
T ss_pred heeeccCcccccc---ceeeeehhhcC--cceeeeeehhhhh
Confidence 3479999996521 11112223332 4467799998743
No 113
>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=46.19 E-value=6.5 Score=26.50 Aligned_cols=13 Identities=31% Similarity=0.692 Sum_probs=6.9
Q ss_pred cCCCCCCCCCHHH
Q 028852 48 PCPYCYEDFDIAS 60 (202)
Q Consensus 48 ~CPfC~e~~dv~~ 60 (202)
.||.|+.+||...
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999999887654
No 114
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=45.94 E-value=13 Score=24.28 Aligned_cols=28 Identities=25% Similarity=0.393 Sum_probs=15.5
Q ss_pred cCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 48 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.||.||.-+-..++- .....+||.|...
T Consensus 2 FCp~Cg~~l~~~~~~---------~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGK---------EKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCC---------CCCEEECCcCCCe
Confidence 588887733222110 1236789988753
No 115
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.69 E-value=8.4 Score=35.32 Aligned_cols=42 Identities=26% Similarity=0.522 Sum_probs=26.5
Q ss_pred CCcccCCCCCC--CCCHHHh-hhhcccccCCCCCc-----eecCCCcccc
Q 028852 44 RPDFPCPYCYE--DFDIASL-CSHLEDEHSCESKV-----TVCPICSVKV 85 (202)
Q Consensus 44 ~~~F~CPfC~e--~~dv~~L-~~H~~~eH~~e~~~-----vVCPVCa~~v 85 (202)
...-.||+||+ -+--... |.|+-=+-+..+.- ..||-|.+.+
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 34678999999 3333444 77855444443332 4799998764
No 116
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=45.45 E-value=14 Score=29.41 Aligned_cols=28 Identities=21% Similarity=0.428 Sum_probs=22.6
Q ss_pred ceecCCCcccc-----hhhhhhhhhhcccchhh
Q 028852 75 VTVCPICSVKV-----ARDMLSHITLQHGHLFK 102 (202)
Q Consensus 75 ~vVCPVCa~~v-----s~d~i~Hl~~~H~~~~k 102 (202)
.+.||+|.... ...+..||+.-||-+-+
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s~ 57 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISST 57 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhccccccC
Confidence 78999998542 55799999999998763
No 117
>PRK11595 DNA utilization protein GntX; Provisional
Probab=45.41 E-value=10 Score=32.54 Aligned_cols=34 Identities=24% Similarity=0.508 Sum_probs=19.8
Q ss_pred cCCCCCCCCCH--HHhhhhcccccCCCCCceecCCCcc
Q 028852 48 PCPYCYEDFDI--ASLCSHLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 48 ~CPfC~e~~dv--~~L~~H~~~eH~~e~~~vVCPVCa~ 83 (202)
.|++|+..+.. ..||.+|...=..- ...||.|..
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg~ 42 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCGL 42 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCCC
Confidence 48888875432 35788776553321 235776654
No 118
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=45.38 E-value=10 Score=29.77 Aligned_cols=14 Identities=50% Similarity=0.904 Sum_probs=11.7
Q ss_pred cccCCCCCCCCCHH
Q 028852 46 DFPCPYCYEDFDIA 59 (202)
Q Consensus 46 ~F~CPfC~e~~dv~ 59 (202)
.-.||+|++.|+-+
T Consensus 47 ~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 47 DTICPKCGEELDSA 60 (102)
T ss_pred cccCCCCCCccCce
Confidence 67899999988754
No 119
>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=45.03 E-value=14 Score=21.94 Aligned_cols=21 Identities=33% Similarity=0.634 Sum_probs=14.0
Q ss_pred cccCCCCCCCCC-HHHhhhhcc
Q 028852 46 DFPCPYCYEDFD-IASLCSHLE 66 (202)
Q Consensus 46 ~F~CPfC~e~~d-v~~L~~H~~ 66 (202)
.|.|.+|+..|. ...+..|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 467888877555 666667754
No 120
>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=44.86 E-value=9.8 Score=26.33 Aligned_cols=10 Identities=40% Similarity=1.228 Sum_probs=8.5
Q ss_pred CcccCCCCCC
Q 028852 45 PDFPCPYCYE 54 (202)
Q Consensus 45 ~~F~CPfC~e 54 (202)
-.|.||+|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 3899999986
No 121
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=44.85 E-value=4.8 Score=31.29 Aligned_cols=30 Identities=23% Similarity=0.550 Sum_probs=19.3
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
..+..+.|+-|+..|++..... .||-|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~-------------~CP~Cgs~ 95 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFDF-------------SCPRCGSP 95 (113)
T ss_dssp EE--EEEETTTS-EEECHHCCH-------------H-SSSSSS
T ss_pred ecCCcEECCCCCCEEecCCCCC-------------CCcCCcCC
Confidence 4477899999999877665442 29999775
No 122
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=44.65 E-value=11 Score=36.59 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=16.6
Q ss_pred cccccCCCCCceecCCCcccch
Q 028852 65 LEDEHSCESKVTVCPICSVKVA 86 (202)
Q Consensus 65 ~~~eH~~e~~~vVCPVCa~~vs 86 (202)
|......+++.-|||||...||
T Consensus 27 c~~~~~~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 27 CSTDFGAEPNTNVCPVCLGLPG 48 (474)
T ss_pred CCcccCCCCCCCcCccccCCCC
Confidence 4444455778999999999963
No 123
>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=44.23 E-value=8.6 Score=31.43 Aligned_cols=41 Identities=20% Similarity=0.566 Sum_probs=29.3
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhh
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i 90 (202)
..+.|..|+..++...+........ ...||.|...+..|++
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 3589999999888777766544432 2399999998766654
No 124
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=44.11 E-value=13 Score=37.92 Aligned_cols=41 Identities=24% Similarity=0.430 Sum_probs=29.2
Q ss_pred CCCCcccCCCCCCCC----CHHHhhhhcccccCCCCCceecCCCccc
Q 028852 42 DVRPDFPCPYCYEDF----DIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 42 d~~~~F~CPfC~e~~----dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
+....+.||.|+..+ +...|.||--..+ +..+-.||=|...
T Consensus 440 ~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 440 DCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred cCCCcccCCCCCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 455679999997743 3456777744444 5678899999887
No 125
>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=43.29 E-value=7.9 Score=33.24 Aligned_cols=38 Identities=26% Similarity=0.424 Sum_probs=0.0
Q ss_pred ceecCCCcccc-hhhhhhhhhhcccc-hhhhhhhcccccc
Q 028852 75 VTVCPICSVKV-ARDMLSHITLQHGH-LFKLQRRRRLRRV 112 (202)
Q Consensus 75 ~vVCPVCa~~v-s~d~i~Hl~~~H~~-~~k~~r~rr~rr~ 112 (202)
.++||||..+| ...|-.||.+.=-- -||-+|.+-..+.
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi~LlDP~wkEqr~~~~~k~ 207 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRIELLDPRWKEQRDRYEAKR 207 (229)
T ss_dssp ----------------------------------------
T ss_pred cccccccccccccccccccccccccccccccccccccccc
Confidence 47999999986 67899999764332 2444455444443
No 126
>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=42.90 E-value=18 Score=22.93 Aligned_cols=26 Identities=19% Similarity=0.544 Sum_probs=14.9
Q ss_pred CCCceecCCCcccc------hhhhhhhhhhcc
Q 028852 72 ESKVTVCPICSVKV------ARDMLSHITLQH 97 (202)
Q Consensus 72 e~~~vVCPVCa~~v------s~d~i~Hl~~~H 97 (202)
+...+.|-.|...+ +.+|..||...|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 34567777776654 236777775544
No 127
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=42.78 E-value=14 Score=34.54 Aligned_cols=40 Identities=30% Similarity=0.547 Sum_probs=29.8
Q ss_pred CCcccCCCCCCCCC--HHHhhhhcccc-cCC-----CCCceecCCCcc
Q 028852 44 RPDFPCPYCYEDFD--IASLCSHLEDE-HSC-----ESKVTVCPICSV 83 (202)
Q Consensus 44 ~~~F~CPfC~e~~d--v~~L~~H~~~e-H~~-----e~~~vVCPVCa~ 83 (202)
...-.||.||...| +.+||.=|--+ |+. +.+..+|+.|-+
T Consensus 4 ~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 4 ASTILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred CcccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCC
Confidence 34678999999887 88888877655 544 344578999975
No 128
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=42.65 E-value=15 Score=33.26 Aligned_cols=40 Identities=25% Similarity=0.602 Sum_probs=27.5
Q ss_pred CCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhhhh
Q 028852 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSH 92 (202)
Q Consensus 43 ~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i~H 92 (202)
......||.|+.. + + +.+ ++...+||.-|-..+..+++.+
T Consensus 8 ~~~~~~Cp~Cg~~-~---i---v~d---~~~Ge~vC~~CG~Vl~e~~iD~ 47 (310)
T PRK00423 8 EEEKLVCPECGSD-K---L---IYD---YERGEIVCADCGLVIEENIIDQ 47 (310)
T ss_pred cccCCcCcCCCCC-C---e---eEE---CCCCeEeecccCCccccccccc
Confidence 3345689999861 1 1 112 3577899999999988877754
No 129
>PF14279 HNH_5: HNH endonuclease
Probab=42.29 E-value=8.7 Score=27.90 Aligned_cols=44 Identities=20% Similarity=0.436 Sum_probs=24.4
Q ss_pred CCCCCCCCCHHHh-hhhcccccCC---CCCceecCCCcccchhhhhhhh
Q 028852 49 CPYCYEDFDIASL-CSHLEDEHSC---ESKVTVCPICSVKVARDMLSHI 93 (202)
Q Consensus 49 CPfC~e~~dv~~L-~~H~~~eH~~---e~~~vVCPVCa~~vs~d~i~Hl 93 (202)
|.||.++.+.... .+|+--+=-. ..+. ||--|-...+.++-.++
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN-VCDKCNNKFGSKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc-hhHHHhHHHhHHHHHHH
Confidence 8999987655432 2333222111 2234 88888888765444443
No 130
>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=41.66 E-value=15 Score=24.02 Aligned_cols=11 Identities=36% Similarity=0.857 Sum_probs=8.6
Q ss_pred CCcccCCCCCC
Q 028852 44 RPDFPCPYCYE 54 (202)
Q Consensus 44 ~~~F~CPfC~e 54 (202)
+..|.||+|+-
T Consensus 16 ~~g~~CP~Cg~ 26 (46)
T PF12760_consen 16 PDGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCCC
Confidence 45689999985
No 131
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.22 E-value=9.1 Score=35.89 Aligned_cols=39 Identities=26% Similarity=0.586 Sum_probs=31.1
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCC---------CceecCCCcccc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCES---------KVTVCPICSVKV 85 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~---------~~vVCPVCa~~v 85 (202)
+.|-.|-|+|...+.+.++-=.|.|-. +--.||||-..+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 999999999998888888877777732 235699998765
No 132
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=40.88 E-value=14 Score=31.45 Aligned_cols=32 Identities=19% Similarity=0.542 Sum_probs=22.4
Q ss_pred CCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
...|.||-|..-+...+=+.+ .-.||.|-+.+
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~~----------~F~Cp~Cg~~L 142 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAMEL----------GFTCPKCGEDL 142 (176)
T ss_pred CCceeCCCCCCcccHHHHHHh----------CCCCCCCCchh
Confidence 457999999884444444433 16899999876
No 133
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.39 E-value=12 Score=33.25 Aligned_cols=45 Identities=27% Similarity=0.571 Sum_probs=31.7
Q ss_pred CCcccCCCCCC--CCCHHHhhhhcccccC------CCCCceecCCCcccchhh
Q 028852 44 RPDFPCPYCYE--DFDIASLCSHLEDEHS------CESKVTVCPICSVKVARD 88 (202)
Q Consensus 44 ~~~F~CPfC~e--~~dv~~L~~H~~~eH~------~e~~~vVCPVCa~~vs~d 88 (202)
-..|.|-.|.+ .==|+.||-|+-==-+ .......||||-+.|+.+
T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~ 97 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID 97 (230)
T ss_pred CCceeeeeeccccCCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence 45799999987 5558899999632111 134567899999988554
No 134
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=40.19 E-value=8.5 Score=29.56 Aligned_cols=16 Identities=13% Similarity=0.673 Sum_probs=12.4
Q ss_pred CCCCcccCCCCCC-CCC
Q 028852 42 DVRPDFPCPYCYE-DFD 57 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~d 57 (202)
-+.+.|.|+|||+ .+-
T Consensus 32 ~Qhaky~CsfCGK~~vK 48 (92)
T KOG0402|consen 32 QQHAKYTCSFCGKKTVK 48 (92)
T ss_pred HHhhhhhhhhcchhhhh
Confidence 4567899999998 443
No 135
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=40.04 E-value=12 Score=29.85 Aligned_cols=64 Identities=14% Similarity=0.306 Sum_probs=33.2
Q ss_pred CCCCCCCCCHHHhhh-hcccccCCCCCceecCCCcccc-hhhhhhhhhhcccchhhhhhhccccccCCCchhhH
Q 028852 49 CPYCYEDFDIASLCS-HLEDEHSCESKVTVCPICSVKV-ARDMLSHITLQHGHLFKLQRRRRLRRVAIPSSQAL 120 (202)
Q Consensus 49 CPfC~e~~dv~~L~~-H~~~eH~~e~~~vVCPVCa~~v-s~d~i~Hl~~~H~~~~k~~r~rr~rr~~~p~~stl 120 (202)
||.|+..+-+..|.| ||... .+...-.|++|.-.. -.+|+.-+....|++-++.+ .-|++| .|.
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~--i~G~F~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~e~-----~lgiSY-PTv 66 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTE--IEGEFELPWFARLSPEQLEFIKLFIKNRGNLKEMEK-----ELGISY-PTV 66 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCE--EEeeeccchhhcCCHHHHHHHHHHHHhcCCHHHHHH-----HHCCCc-HHH
Confidence 999998877665521 22211 122222333332222 34677777777777655532 234564 765
No 136
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=39.96 E-value=15 Score=25.84 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=9.1
Q ss_pred CCcccCCCCCC
Q 028852 44 RPDFPCPYCYE 54 (202)
Q Consensus 44 ~~~F~CPfC~e 54 (202)
+..|.||.||.
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 56899999975
No 137
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=39.48 E-value=13 Score=28.23 Aligned_cols=37 Identities=16% Similarity=0.321 Sum_probs=19.7
Q ss_pred CCCCCCCCCHHHhhhhccccc----CCCCCceecCCCcccc
Q 028852 49 CPYCYEDFDIASLCSHLEDEH----SCESKVTVCPICSVKV 85 (202)
Q Consensus 49 CPfC~e~~dv~~L~~H~~~eH----~~e~~~vVCPVCa~~v 85 (202)
||+|+.+.-+.....+.-..- .++....+||.|-...
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 999986333333333321111 1133456799997764
No 138
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=39.46 E-value=14 Score=36.48 Aligned_cols=22 Identities=27% Similarity=0.472 Sum_probs=17.1
Q ss_pred cccccCCCCCceecCCCcccch
Q 028852 65 LEDEHSCESKVTVCPICSVKVA 86 (202)
Q Consensus 65 ~~~eH~~e~~~vVCPVCa~~vs 86 (202)
|..+...+++.-|||||...||
T Consensus 83 c~~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 83 CPYNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred CCcccCCCCccCcCccccCCCC
Confidence 4445556889999999999973
No 139
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=39.44 E-value=18 Score=32.76 Aligned_cols=43 Identities=16% Similarity=0.404 Sum_probs=28.6
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhhhhhhhcccc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHGH 99 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i~Hl~~~H~~ 99 (202)
..||.|+.. + +..+ ++....||--|...+..+.+.+-.-.+.|
T Consensus 2 ~~CpeCg~~-~-------~~~d--~~~ge~VC~~CG~Vi~~~~id~gpewr~f 44 (285)
T COG1405 2 MSCPECGST-N-------IITD--YERGEIVCADCGLVLEDSLIDPGPEWRAF 44 (285)
T ss_pred CCCCCCCCc-c-------ceee--ccCCeEEeccCCEEeccccccCCCCcccc
Confidence 479999885 1 1112 23567899999998877777655444444
No 140
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=39.14 E-value=25 Score=33.63 Aligned_cols=49 Identities=27% Similarity=0.521 Sum_probs=33.6
Q ss_pred CcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc--hhhhhhhhh
Q 028852 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHIT 94 (202)
Q Consensus 45 ~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v--s~d~i~Hl~ 94 (202)
..|+||.|+- ==..++|..|+.-.|.- .+.--|--|...- -.|+..|+.
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 3688888877 33467788888888876 6777788877663 335555554
No 141
>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=39.10 E-value=3.8 Score=25.45 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=4.5
Q ss_pred CCceecCCC
Q 028852 73 SKVTVCPIC 81 (202)
Q Consensus 73 ~~~vVCPVC 81 (202)
...+.||+|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 334446655
No 142
>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=39.08 E-value=21 Score=29.14 Aligned_cols=31 Identities=19% Similarity=0.367 Sum_probs=22.8
Q ss_pred CCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
++-....||-||. -+|+ ...++|||-|....
T Consensus 5 elGtKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~ 36 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDL-------------NRRPAVSPYTGEQF 36 (129)
T ss_pred hhCccccCCCcCcccccc-------------CCCCccCCCcCCcc
Confidence 4556789999998 4442 34689999998864
No 143
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.96 E-value=19 Score=38.38 Aligned_cols=36 Identities=19% Similarity=0.405 Sum_probs=17.1
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
.|.||.||..-...--|..|.. ......||-|-..+
T Consensus 638 ~frCP~CG~~Te~i~fCP~CG~----~~~~y~CPKCG~El 673 (1121)
T PRK04023 638 YRRCPFCGTHTEPVYRCPRCGI----EVEEDECEKCGREP 673 (1121)
T ss_pred cccCCCCCCCCCcceeCccccC----cCCCCcCCCCCCCC
Confidence 4555555553333334444422 22234577776654
No 144
>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=38.56 E-value=12 Score=35.87 Aligned_cols=33 Identities=36% Similarity=0.950 Sum_probs=15.1
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCC-cccchhhhh
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPIC-SVKVARDML 90 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVC-a~~vs~d~i 90 (202)
+...||||+-.+ |+ +-+--+|||| .+.||.+-+
T Consensus 379 ~~v~CP~cgA~y------------~~-~~kG~lC~vC~l~~IG~~a~ 412 (422)
T PF06957_consen 379 PSVKCPYCGAKY------------HP-EYKGQLCPVCELSEIGADAS 412 (422)
T ss_dssp -EEE-TTT--EE------------EG-GGTTSB-TTTTTBBTT---S
T ss_pred CCeeCCCCCCcc------------Ch-hhCCCCCCCCcceeeCCcce
Confidence 346699997633 22 2345699999 455666544
No 145
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=38.48 E-value=18 Score=25.83 Aligned_cols=46 Identities=24% Similarity=0.492 Sum_probs=21.6
Q ss_pred CCCCcccCC--CCCCCCCHHHhhhhcccccC----CCCCceecCCCcccchh
Q 028852 42 DVRPDFPCP--YCYEDFDIASLCSHLEDEHS----CESKVTVCPICSVKVAR 87 (202)
Q Consensus 42 d~~~~F~CP--fC~e~~dv~~L~~H~~~eH~----~e~~~vVCPVCa~~vs~ 87 (202)
+..+...|| -|+.-|-..=|......... +....+.||.|...++-
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 344578887 88888888888888765443 34556789999987643
No 146
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.48 E-value=12 Score=29.29 Aligned_cols=31 Identities=29% Similarity=0.612 Sum_probs=21.5
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
+.+..+.|+-|+..|..... ....||-|...
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 45678999999976655422 22459999864
No 147
>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=37.17 E-value=17 Score=35.39 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=13.4
Q ss_pred CCCceecCCCcccch
Q 028852 72 ESKVTVCPICSVKVA 86 (202)
Q Consensus 72 e~~~vVCPVCa~~vs 86 (202)
+++.-|||||...||
T Consensus 34 ~PNt~v~pvclg~PG 48 (478)
T TIGR00133 34 PPNTNVCPVCLGLPG 48 (478)
T ss_pred CCCcccCccccCCCC
Confidence 789999999999974
No 148
>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=36.77 E-value=13 Score=36.09 Aligned_cols=48 Identities=33% Similarity=0.453 Sum_probs=34.7
Q ss_pred CCCHHHhhhhcccccCCCC-----------------CceecCCCcccc--hhhhhhhhhhcccchhh
Q 028852 55 DFDIASLCSHLEDEHSCES-----------------KVTVCPICSVKV--ARDMLSHITLQHGHLFK 102 (202)
Q Consensus 55 ~~dv~~L~~H~~~eH~~e~-----------------~~vVCPVCa~~v--s~d~i~Hl~~~H~~~~k 102 (202)
.+.+..|..|+...|..++ +..+||+|..+. ...+..||-..|-..++
T Consensus 20 kVsi~eL~sy~~~~~~~~a~~~Lseal~fak~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 20 KVSIDELKSYYESVYDREAADALSEALSFAKENKSWRFWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eeEHHHHHHHHHhccchHHHHHHHHHHHHHHhcCceeEeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 3456777777776654322 246799999775 67899999999988764
No 149
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.70 E-value=10 Score=30.75 Aligned_cols=38 Identities=29% Similarity=0.660 Sum_probs=22.2
Q ss_pred CcccCCCCCCCCCHH-Hh-hhhcccccCCCC---CceecCCCc
Q 028852 45 PDFPCPYCYEDFDIA-SL-CSHLEDEHSCES---KVTVCPICS 82 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~-~L-~~H~~~eH~~e~---~~vVCPVCa 82 (202)
..+.||+|.+.|... .| |-|---..+... ....||+|.
T Consensus 12 ~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccC
Confidence 479999998866555 22 233222212111 348999999
No 150
>PF02934 GatB_N: GatB/GatE catalytic domain; InterPro: IPR006075 Glutamyl-tRNA(Gln) amidotransferase subunit B (6.3.5 from EC) [] is a microbial enzyme that furnishes a means for formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The enzyme is composed of three subunits: A (an amidase), B and C. It also exists in eukaryotes as a protein targeted to the mitochondria. ; GO: 0016874 ligase activity; PDB: 3H0M_H 3H0R_K 3H0L_K 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B 2G5H_B 2DQN_B ....
Probab=36.38 E-value=19 Score=33.01 Aligned_cols=26 Identities=27% Similarity=0.530 Sum_probs=17.5
Q ss_pred hhhhcccccCCCCCceecCCCcccch
Q 028852 61 LCSHLEDEHSCESKVTVCPICSVKVA 86 (202)
Q Consensus 61 L~~H~~~eH~~e~~~vVCPVCa~~vs 86 (202)
|.|.|......+++.-|||||...||
T Consensus 18 lFc~c~~~~~~~pNt~v~~~~lg~PG 43 (289)
T PF02934_consen 18 LFCSCPNEFGAEPNTNVCPVCLGLPG 43 (289)
T ss_dssp SSSSSBSSTTSCTTSSB-TTTTT-TT
T ss_pred CCCCCCCCCCCCCccccCceeccCCC
Confidence 34445666566789999999999974
No 151
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=36.34 E-value=22 Score=32.29 Aligned_cols=29 Identities=28% Similarity=0.557 Sum_probs=22.2
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
-..||-|++-+-...|-.. ..|||-|...
T Consensus 26 ~~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERN----------LEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHhh----------CCCCCCCCCc
Confidence 4679999997777666543 4799999875
No 152
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=36.31 E-value=15 Score=34.38 Aligned_cols=40 Identities=28% Similarity=0.498 Sum_probs=26.7
Q ss_pred cccCCCCCCCCCHHHhhhhccccc-CCCCCceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEH-SCESKVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH-~~e~~~vVCPVCa~~v 85 (202)
.-.||+|+-+--....|++|-... +.+-.+.+|.+|...+
T Consensus 136 ~g~CP~C~~~~a~g~~Ce~cG~~~~~~~l~~p~~~~~g~~~ 176 (391)
T PF09334_consen 136 EGTCPYCGSDKARGDQCENCGRPLEPEELINPVCKICGSPP 176 (391)
T ss_dssp TCEETTT--SSCTTTEETTTSSBEECCCSECEEETTTS-B-
T ss_pred eccccCcCccccCCCcccCCCCCcccccccCCccccccccC
Confidence 367999986555667777776544 3577889999998875
No 153
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=36.12 E-value=21 Score=34.94 Aligned_cols=42 Identities=29% Similarity=0.585 Sum_probs=27.2
Q ss_pred CCcccCCCCCCCCCHHHhhhhcccc--cCCCCCceecCCCcccchh
Q 028852 44 RPDFPCPYCYEDFDIASLCSHLEDE--HSCESKVTVCPICSVKVAR 87 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~~L~~H~~~e--H~~e~~~vVCPVCa~~vs~ 87 (202)
+-..+||-|++.+.+. ..++.-. ...+.-..+||-|-..+..
T Consensus 198 ~~~vpCPhCg~~~~l~--~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLE--WENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEEccCCCCCCCcccc--ccceeecCCCCccceEEECCCCcCCCCH
Confidence 4568999999955443 2222222 1345566899999998855
No 154
>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=35.55 E-value=18 Score=27.52 Aligned_cols=8 Identities=63% Similarity=1.767 Sum_probs=5.3
Q ss_pred ccCCCCCC
Q 028852 47 FPCPYCYE 54 (202)
Q Consensus 47 F~CPfC~e 54 (202)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 46777774
No 155
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=35.51 E-value=22 Score=32.65 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=22.3
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
-..||-|+.-+-...|-.. ..|||-|...
T Consensus 38 w~kc~~C~~~~~~~~l~~~----------~~vcp~c~~h 66 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSK----------MNICEQCGYH 66 (296)
T ss_pred eeECCCccchhhHHHHHHc----------CCCCCCCCCC
Confidence 4679999997777776543 5799999875
No 156
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=35.40 E-value=22 Score=32.32 Aligned_cols=29 Identities=28% Similarity=0.559 Sum_probs=21.9
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
-..||-|+.-+-...|-.. ..|||-|...
T Consensus 27 ~~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEAN----------LNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHhc----------CCCCCCCCCC
Confidence 4789999997766666443 4699999775
No 157
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=35.03 E-value=8.5 Score=29.61 Aligned_cols=33 Identities=24% Similarity=0.604 Sum_probs=22.5
Q ss_pred CCCCCCcccCCCCCCC-CCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 40 EDDVRPDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 40 ~dd~~~~F~CPfC~e~-~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
|..+++.+.||+|+.. +. +..+.--.|.-|-..
T Consensus 29 e~~~~~~~~Cp~C~~~~Vk------------R~a~GIW~C~kCg~~ 62 (89)
T COG1997 29 EAQQRAKHVCPFCGRTTVK------------RIATGIWKCRKCGAK 62 (89)
T ss_pred HHHHhcCCcCCCCCCccee------------eeccCeEEcCCCCCe
Confidence 3367889999999873 22 233556678888665
No 158
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.83 E-value=24 Score=38.41 Aligned_cols=34 Identities=29% Similarity=0.726 Sum_probs=16.8
Q ss_pred cccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.|.||-||. .+. ..|..|-.. .+. ...||.|-+.
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~--te~-vy~CPsCGae 701 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTH--TEP-VYVCPDCGAE 701 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCc--CCC-ceeCccCCCc
Confidence 577777777 332 255544433 111 2355555554
No 159
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.00 E-value=21 Score=34.04 Aligned_cols=15 Identities=33% Similarity=0.811 Sum_probs=10.6
Q ss_pred CcccCCCCCCCCCHH
Q 028852 45 PDFPCPYCYEDFDIA 59 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~ 59 (202)
.+|+||||-.+-+..
T Consensus 373 ~sfKCPYCP~e~~~~ 387 (394)
T KOG2817|consen 373 QSFKCPYCPVEQLAS 387 (394)
T ss_pred eeeeCCCCCcccCHH
Confidence 369999997755443
No 160
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The presence of motifs with seven invariant Cys residues in the N-terminal 50 residues, including three instances of CXXC, would be consistent with function as an oxidoreductase with FeS clusters. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon.
Probab=33.64 E-value=19 Score=34.05 Aligned_cols=33 Identities=24% Similarity=0.500 Sum_probs=21.1
Q ss_pred cccCCCCCC--CCCHHHh-hhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYE--DFDIASL-CSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e--~~dv~~L-~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
-..||||+. .-+...| |.||. ..+..||.|...
T Consensus 10 ~~~C~wC~~p~~~~~~~~~c~~C~------~~~~~C~yC~~~ 45 (404)
T TIGR03278 10 RGFCRYCYFKKVDDEQPFGCKNCP------PGTKGCDYCTRS 45 (404)
T ss_pred CCcCCCCCCCCCCCCCCCCCCcCC------CCCCCCCCCCch
Confidence 468999987 3334444 55543 236789999665
No 161
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=33.57 E-value=23 Score=33.86 Aligned_cols=42 Identities=17% Similarity=0.413 Sum_probs=26.2
Q ss_pred Hhhhhccccc-CCCCCceecCCCcccc--hhhhhhhhhhcccchh
Q 028852 60 SLCSHLEDEH-SCESKVTVCPICSVKV--ARDMLSHITLQHGHLF 101 (202)
Q Consensus 60 ~L~~H~~~eH-~~e~~~vVCPVCa~~v--s~d~i~Hl~~~H~~~~ 101 (202)
.+..|..+.| .+.+-...|-+|.... |.++.+||+-+||+-.
T Consensus 336 q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~ 380 (467)
T KOG3608|consen 336 QMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRL 380 (467)
T ss_pred HHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccC
Confidence 3444444444 2333345577776553 7789999999999843
No 162
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=33.57 E-value=10 Score=28.71 Aligned_cols=7 Identities=57% Similarity=1.497 Sum_probs=3.9
Q ss_pred cCCCCCC
Q 028852 48 PCPYCYE 54 (202)
Q Consensus 48 ~CPfC~e 54 (202)
+|||||+
T Consensus 3 ~CP~CG~ 9 (84)
T PF04267_consen 3 PCPHCGP 9 (84)
T ss_dssp EETTTEE
T ss_pred cCCCCCc
Confidence 4555555
No 163
>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=33.12 E-value=28 Score=24.48 Aligned_cols=39 Identities=26% Similarity=0.503 Sum_probs=23.4
Q ss_pred CcccCCCCCCCCCHHHhhh-----------------hcccccCCCCCceecCCCcc
Q 028852 45 PDFPCPYCYEDFDIASLCS-----------------HLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~-----------------H~~~eH~~e~~~vVCPVCa~ 83 (202)
....||+|--.+|-..|+. |.--+........+||.|..
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 4678999977776566555 21112223346789999954
No 164
>PHA02929 N1R/p28-like protein; Provisional
Probab=32.81 E-value=13 Score=33.08 Aligned_cols=42 Identities=24% Similarity=0.501 Sum_probs=24.4
Q ss_pred CCcccCCCCCCCCCHH----------HhhhhcccccCC---CCCceecCCCcccc
Q 028852 44 RPDFPCPYCYEDFDIA----------SLCSHLEDEHSC---ESKVTVCPICSVKV 85 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~----------~L~~H~~~eH~~---e~~~vVCPVCa~~v 85 (202)
.....||.|.+.+... .=|.|.--..+. -.....||+|...+
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 125553222221 12356899998754
No 165
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=31.88 E-value=34 Score=37.00 Aligned_cols=46 Identities=20% Similarity=0.490 Sum_probs=31.5
Q ss_pred cCCCcCCCCCCCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 32 LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 32 ~~~~~~~~~dd~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
+||-|+++ +++-|.||-|.- +|...+-. -=-++--.-.||.|....
T Consensus 672 lgITeVdP---L~phy~c~~c~~~ef~~~~~~-----~sg~dlp~k~cp~c~~~~ 718 (1213)
T TIGR01405 672 TGITEVNP---LPPHYLCPNCKYSEFITDGSV-----GSGFDLPDKDCPKCGAPL 718 (1213)
T ss_pred hcCCCcCC---CcccccCcccccccccccccc-----cccccCccccCccccccc
Confidence 58877776 788999999966 66544311 112444567899998874
No 166
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=31.85 E-value=23 Score=29.82 Aligned_cols=40 Identities=23% Similarity=0.558 Sum_probs=25.4
Q ss_pred cccCCCCCCCCCHHHhhhhccccc-----CCCC-CceecCCCcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEH-----SCES-KVTVCPICSVKV 85 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH-----~~e~-~~vVCPVCa~~v 85 (202)
--.||.|+..++...-..|++=.| .... +-+.|+-|-...
T Consensus 20 ~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~TG~VRGLLC~~CN~~l 65 (157)
T PHA02565 20 NGICPLCKRELDGDVSKNHLDHDHELNGPNAGRVRGLLCNLCNALE 65 (157)
T ss_pred CCcCCCCCCccCCCccccccCCCCCCCCcccccccccCchhhhhhh
Confidence 457999999776432233777777 3222 456699997744
No 167
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=31.83 E-value=21 Score=31.82 Aligned_cols=53 Identities=21% Similarity=0.485 Sum_probs=26.3
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccc--hhhhhhhhhhccc
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQHG 98 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v--s~d~i~Hl~~~H~ 98 (202)
..|+|-.|++.|..+-+..--..-| .+.+...|..|..-. +-|+-+|+...-|
T Consensus 116 d~ftCrvCgK~F~lQRmlnrh~kch-~~vkr~lct~cgkgfndtfdlkrh~rthtg 170 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQRMLNRHLKCH-SDVKRHLCTFCGKGFNDTFDLKRHTRTHTG 170 (267)
T ss_pred CeeeeehhhhhhhHHHHHHHHhhhc-cHHHHHHHhhccCcccchhhhhhhhccccC
Confidence 4677777777776665543212222 223344555555443 3355555544444
No 168
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=31.30 E-value=16 Score=31.35 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=0.0
Q ss_pred cccCCCCCCCCCHHHhhhhcccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDE 68 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~e 68 (202)
...||+||+-+-+..+-.|+.-.
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi~ 190 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRIE 190 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 48999999999999999997643
No 169
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.45 E-value=30 Score=23.27 Aligned_cols=32 Identities=19% Similarity=0.564 Sum_probs=18.7
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCC
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPIC 81 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVC 81 (202)
....-+.||.|+-.+...- .. +. .....||.|
T Consensus 24 ~~~v~W~C~~Cgh~w~~~v-~~------R~-~~~~~CP~C 55 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWKASV-ND------RT-RRGKGCPYC 55 (55)
T ss_pred CCEEEEECCCCCCeeEccH-hh------hc-cCCCCCCCC
Confidence 3345699999976443221 11 11 456789988
No 170
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=30.45 E-value=16 Score=28.48 Aligned_cols=31 Identities=19% Similarity=0.534 Sum_probs=20.2
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
..+..+.|+-|+..|.... .....||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~------------~~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLT------------QRVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCCeeecCC------------ccCCcCcCcCCC
Confidence 4577899999987443321 112579999864
No 171
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=30.29 E-value=19 Score=22.90 Aligned_cols=28 Identities=29% Similarity=0.762 Sum_probs=15.6
Q ss_pred cCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 48 ~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.||-|+..+....+ .+-..-+||-|.-.
T Consensus 1 ~CP~C~~~l~~~~~---------~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRL---------GDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEE---------CCEEEEECCCCCeE
Confidence 37777665554444 22334467777543
No 172
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=30.22 E-value=14 Score=36.05 Aligned_cols=37 Identities=32% Similarity=0.732 Sum_probs=20.7
Q ss_pred CcccCCCCCCCCCHHH------hhhhcccccCC---CCCceecCCCcc
Q 028852 45 PDFPCPYCYEDFDIAS------LCSHLEDEHSC---ESKVTVCPICSV 83 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~------L~~H~~~eH~~---e~~~vVCPVCa~ 83 (202)
.-=+||.|-|-+|... ||.| ..|+. --...-||||.-
T Consensus 174 ELPTCpVCLERMD~s~~gi~t~~c~H--sfh~~cl~~w~~~scpvcR~ 219 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSSTTGILTILCNH--SFHCSCLMKWWDSSCPVCRY 219 (493)
T ss_pred cCCCcchhHhhcCccccceeeeeccc--ccchHHHhhcccCcChhhhh
Confidence 4468999988555443 4555 22221 113456777743
No 173
>PHA00733 hypothetical protein
Probab=30.14 E-value=34 Score=27.25 Aligned_cols=25 Identities=24% Similarity=0.483 Sum_probs=21.4
Q ss_pred cccCCCCCCC-CCHHHhhhhcccccC
Q 028852 46 DFPCPYCYED-FDIASLCSHLEDEHS 70 (202)
Q Consensus 46 ~F~CPfC~e~-~dv~~L~~H~~~eH~ 70 (202)
.|.|+.|++. -....|..|+...|.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 5999999994 566889999999886
No 174
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=30.05 E-value=26 Score=29.84 Aligned_cols=13 Identities=46% Similarity=0.958 Sum_probs=10.5
Q ss_pred ccCCCCCCCCCHH
Q 028852 47 FPCPYCYEDFDIA 59 (202)
Q Consensus 47 F~CPfC~e~~dv~ 59 (202)
=+||+|+.-+|-.
T Consensus 155 P~CPlCg~PlDP~ 167 (171)
T PF11290_consen 155 PPCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCCC
Confidence 4799999987754
No 175
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=29.89 E-value=23 Score=29.44 Aligned_cols=32 Identities=22% Similarity=0.587 Sum_probs=18.0
Q ss_pred ccCCCCCCCC-CHHHhhhhcccccCCCCC-----ceecCCCcccc
Q 028852 47 FPCPYCYEDF-DIASLCSHLEDEHSCESK-----VTVCPICSVKV 85 (202)
Q Consensus 47 F~CPfC~e~~-dv~~L~~H~~~eH~~e~~-----~vVCPVCa~~v 85 (202)
..|||||... .+. +.-..... .--||-|....
T Consensus 1 m~cp~c~~~~~~~~-------~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVI-------DSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeE-------eccccCCCCceeeeeeccccCCcc
Confidence 3699999733 222 22222222 24599998864
No 176
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=29.83 E-value=18 Score=33.27 Aligned_cols=18 Identities=22% Similarity=0.615 Sum_probs=14.2
Q ss_pred CceecCCCcccchhhhhh
Q 028852 74 KVTVCPICSVKVARDMLS 91 (202)
Q Consensus 74 ~~vVCPVCa~~vs~d~i~ 91 (202)
+..+||||..+|...||.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 457999999999776763
No 177
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=29.79 E-value=21 Score=35.92 Aligned_cols=54 Identities=26% Similarity=0.560 Sum_probs=33.7
Q ss_pred CCCCCCcccCCCCCC-CCC-HHHhhhh-----ccc---ccCCCCCceecCCCcccchhhhhhhh
Q 028852 40 EDDVRPDFPCPYCYE-DFD-IASLCSH-----LED---EHSCESKVTVCPICSVKVARDMLSHI 93 (202)
Q Consensus 40 ~dd~~~~F~CPfC~e-~~d-v~~L~~H-----~~~---eH~~e~~~vVCPVCa~~vs~d~i~Hl 93 (202)
.+|-....-|-+|.+ -=| +.+-|.| |.. +-..+..+|.||+|...++.|+..|-
T Consensus 530 ~~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred CccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 345566788999976 222 3333333 221 22247778999999998877765554
No 178
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=29.57 E-value=19 Score=25.90 Aligned_cols=36 Identities=17% Similarity=0.603 Sum_probs=21.4
Q ss_pred ccCCCCCC-CCCHHHh------hhhc-ccccCCCCCceecCCCcc
Q 028852 47 FPCPYCYE-DFDIASL------CSHL-EDEHSCESKVTVCPICSV 83 (202)
Q Consensus 47 F~CPfC~e-~~dv~~L------~~H~-~~eH~~e~~~vVCPVCa~ 83 (202)
|.||-|+. +++...+ ...+ +-+|. .-..++|+-|.-
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~-~f~~v~C~~CGY 44 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNK-KFTTVSCTNCGY 44 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCc-EEEEEECCCCCC
Confidence 67999987 6665543 2222 22222 234688999964
No 179
>PF14369 zf-RING_3: zinc-finger
Probab=29.19 E-value=27 Score=22.06 Aligned_cols=9 Identities=44% Similarity=1.228 Sum_probs=7.6
Q ss_pred cCCCCCCCC
Q 028852 48 PCPYCYEDF 56 (202)
Q Consensus 48 ~CPfC~e~~ 56 (202)
.||.|+-+|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 799998765
No 180
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=28.87 E-value=40 Score=37.09 Aligned_cols=46 Identities=22% Similarity=0.545 Sum_probs=31.1
Q ss_pred cCCCcCCCCCCCCCcccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc
Q 028852 32 LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (202)
Q Consensus 32 ~~~~~~~~~dd~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v 85 (202)
+||-++++ +++-|.||-|.- +|...+-. -=.++--.-.||.|-+..
T Consensus 897 lgITeVdP---L~phy~C~~C~~~ef~~~~~~-----~sG~Dlpdk~Cp~Cg~~~ 943 (1437)
T PRK00448 897 IGITEVNP---LPPHYVCPNCKYSEFFTDGSV-----GSGFDLPDKDCPKCGTKL 943 (1437)
T ss_pred hcCCCcCC---CCccccCcccccccccccccc-----cccccCccccCccccccc
Confidence 68888776 789999999965 66543310 112344456899998874
No 181
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=28.66 E-value=41 Score=28.55 Aligned_cols=41 Identities=15% Similarity=0.314 Sum_probs=25.0
Q ss_pred ccCCCCCC---CCCHHHhhhhcccccCC-CCCceecCCCccc--chh
Q 028852 47 FPCPYCYE---DFDIASLCSHLEDEHSC-ESKVTVCPICSVK--VAR 87 (202)
Q Consensus 47 F~CPfC~e---~~dv~~L~~H~~~eH~~-e~~~vVCPVCa~~--vs~ 87 (202)
=.||+|+- .+...+-..-+...|.- .....+||.|-.. +|.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~Gs 144 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGS 144 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCch
Confidence 46999976 45555544444444443 2345779999876 454
No 182
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=28.57 E-value=26 Score=25.77 Aligned_cols=8 Identities=50% Similarity=1.464 Sum_probs=6.3
Q ss_pred ccCCCCCC
Q 028852 47 FPCPYCYE 54 (202)
Q Consensus 47 F~CPfC~e 54 (202)
|.||+|+.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 67888876
No 183
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.47 E-value=24 Score=33.23 Aligned_cols=10 Identities=60% Similarity=1.447 Sum_probs=8.5
Q ss_pred CcccCCCCCC
Q 028852 45 PDFPCPYCYE 54 (202)
Q Consensus 45 ~~F~CPfC~e 54 (202)
.+|.||||-+
T Consensus 375 ~~FKCPYCP~ 384 (396)
T COG5109 375 LSFKCPYCPE 384 (396)
T ss_pred EEeeCCCCCc
Confidence 3799999977
No 184
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.45 E-value=30 Score=24.99 Aligned_cols=13 Identities=38% Similarity=0.976 Sum_probs=9.2
Q ss_pred CCCceecCCCccc
Q 028852 72 ESKVTVCPICSVK 84 (202)
Q Consensus 72 e~~~vVCPVCa~~ 84 (202)
+...|+||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 5667788888764
No 185
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=27.98 E-value=26 Score=30.29 Aligned_cols=20 Identities=30% Similarity=0.629 Sum_probs=16.7
Q ss_pred eecCCCcccc--hhhhhhhhhh
Q 028852 76 TVCPICSVKV--ARDMLSHITL 95 (202)
Q Consensus 76 vVCPVCa~~v--s~d~i~Hl~~ 95 (202)
..|-||...| +.||+.||+.
T Consensus 76 yyCdVCdcvvKDSinflDHiNg 97 (193)
T KOG4727|consen 76 YYCDVCDCVVKDSINFLDHING 97 (193)
T ss_pred eeeeecceeehhhHHHHHHhcc
Confidence 3499998887 7899999975
No 186
>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=27.98 E-value=21 Score=23.47 Aligned_cols=9 Identities=44% Similarity=1.180 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 028852 46 DFPCPYCYE 54 (202)
Q Consensus 46 ~F~CPfC~e 54 (202)
.-.||||+.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 689999985
No 187
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=27.92 E-value=21 Score=32.72 Aligned_cols=43 Identities=21% Similarity=0.559 Sum_probs=24.7
Q ss_pred CCCCcccCCCCCC-CCCHHHhhhhcccccCC-----CCCceecCCCccc
Q 028852 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSC-----ESKVTVCPICSVK 84 (202)
Q Consensus 42 d~~~~F~CPfC~e-~~dv~~L~~H~~~eH~~-----e~~~vVCPVCa~~ 84 (202)
+..--..|=||-- +=..+-+-.|....--. --+..|||||.+.
T Consensus 229 ~Q~r~l~CvFC~nN~E~~A~y~tH~lkd~dgRVLCPkLR~YVCPiCGAT 277 (318)
T KOG4602|consen 229 NQPRPLCCVFCFNNAEEFARYHTHPLKDKDGRVLCPKLRSYVCPICGAT 277 (318)
T ss_pred CCCCceeEEeecCCCchhhheecccccCCCCcEechhHhhhcCcccccc
Confidence 3344458999966 44555555665443221 1234678889774
No 188
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.84 E-value=37 Score=31.76 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=20.3
Q ss_pred CCCCCcccCCCCCCCCCHHHhhhh
Q 028852 41 DDVRPDFPCPYCYEDFDIASLCSH 64 (202)
Q Consensus 41 dd~~~~F~CPfC~e~~dv~~L~~H 64 (202)
+-+...|+||.|+..|-..+|-.|
T Consensus 15 ~q~~~~fpc~ic~r~f~~~~L~kh 38 (351)
T KOG3940|consen 15 AQMQMRFPCRICQREFRRRELMKH 38 (351)
T ss_pred ccccccccccccccchhhhhhhcc
Confidence 345679999999999988888887
No 189
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=27.83 E-value=23 Score=37.00 Aligned_cols=53 Identities=15% Similarity=0.350 Sum_probs=39.6
Q ss_pred cccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCcccc--hhhhhhhhhhcccch
Q 028852 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQHGHL 100 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~v--s~d~i~Hl~~~H~~~ 100 (202)
.-.|-||++ .=..+.|.-|+... ...+..+|-||..+. ..|+--|+.-+|..+
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSH--TGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~ 408 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSH--TGERPFQCNVCGNRFSTKGNLKVHFQRHREKY 408 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhcc--CCCCCeeecccccccccccceeeeeeeccccC
Confidence 345999999 66778899997664 556789999999886 458888875544443
No 190
>PRK10220 hypothetical protein; Provisional
Probab=27.70 E-value=38 Score=27.03 Aligned_cols=26 Identities=23% Similarity=0.754 Sum_probs=16.2
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
=+||-|+.++. .-+....|||-|+.-
T Consensus 4 P~CP~C~seyt------------Y~d~~~~vCpeC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYT------------YEDNGMYICPECAHE 29 (111)
T ss_pred CcCCCCCCcce------------EcCCCeEECCcccCc
Confidence 36888855332 123446899999764
No 191
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=27.55 E-value=25 Score=23.19 Aligned_cols=12 Identities=25% Similarity=0.736 Sum_probs=6.4
Q ss_pred CcccCCCCCCCC
Q 028852 45 PDFPCPYCYEDF 56 (202)
Q Consensus 45 ~~F~CPfC~e~~ 56 (202)
+.-.|-+|+..+
T Consensus 17 ~~a~C~~C~~~l 28 (50)
T smart00614 17 QRAKCKYCGKKL 28 (50)
T ss_pred eEEEecCCCCEe
Confidence 445566665543
No 192
>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=26.68 E-value=18 Score=24.57 Aligned_cols=17 Identities=41% Similarity=0.960 Sum_probs=11.1
Q ss_pred cccCCCCCC-CCCHHHhh
Q 028852 46 DFPCPYCYE-DFDIASLC 62 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~ 62 (202)
.|.||+|.. .-.+..+.
T Consensus 6 d~~Cp~C~~~~~~l~~~~ 23 (98)
T cd02972 6 DPLCPYCYLFEPELEKLL 23 (98)
T ss_pred CCCCHhHHhhhHHHHHHH
Confidence 578999988 44444443
No 193
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=26.32 E-value=29 Score=19.15 Aligned_cols=17 Identities=24% Similarity=0.686 Sum_probs=8.2
Q ss_pred ecCCCcccc--hhhhhhhh
Q 028852 77 VCPICSVKV--ARDMLSHI 93 (202)
Q Consensus 77 VCPVCa~~v--s~d~i~Hl 93 (202)
.|.||-... ...|..|+
T Consensus 2 ~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCcCCHHHHHHHH
Confidence 356664443 23455554
No 194
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.30 E-value=31 Score=32.36 Aligned_cols=24 Identities=29% Similarity=0.847 Sum_probs=20.2
Q ss_pred cccCCCCCCCCCHHHhhhhcccccC
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHS 70 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~ 70 (202)
+.-||||.-.+.....|.|++ -|-
T Consensus 2 e~iCP~CkLsv~~~~m~~Hie-aHF 25 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIE-AHF 25 (393)
T ss_pred cccccceecccCHHHHHHHHH-hhc
Confidence 457999999999999999998 443
No 195
>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=26.13 E-value=20 Score=24.63 Aligned_cols=45 Identities=24% Similarity=0.552 Sum_probs=28.5
Q ss_pred CCCcCCCCC-CCCCcccCCCCCC--CCCHHHhhhhcccccCCCCCceecCCCcccch
Q 028852 33 SIDDFEVED-DVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (202)
Q Consensus 33 ~~~~~~~~d-d~~~~F~CPfC~e--~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs 86 (202)
.++|++.++ +..-.|+| =||- .+....|-.+ .-.|-|+-|+-.+.
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 23478999 5987 6666676665 45677999987653
No 196
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.11 E-value=45 Score=33.99 Aligned_cols=29 Identities=31% Similarity=0.448 Sum_probs=25.4
Q ss_pred CCcccCCCCCC-CCCHHHhhhhcccccCCC
Q 028852 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCE 72 (202)
Q Consensus 44 ~~~F~CPfC~e-~~dv~~L~~H~~~eH~~e 72 (202)
+.---|+||.+ -||..+|..|+..+|.+.
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 44678999999 999999999999998863
No 197
>PF14968 CCDC84: Coiled coil protein 84
Probab=25.94 E-value=33 Score=32.01 Aligned_cols=25 Identities=24% Similarity=0.454 Sum_probs=18.7
Q ss_pred CCCCcccCCCCCCCCCHH-------Hhhhhcc
Q 028852 42 DVRPDFPCPYCYEDFDIA-------SLCSHLE 66 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~-------~L~~H~~ 66 (202)
+-+..|=|+||+.++... +++.|+-
T Consensus 54 ~~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLa 85 (336)
T PF14968_consen 54 EHRNRFWCVFCDCEVREHDSSFACGGAIEHLA 85 (336)
T ss_pred cccceeEeeCccchhhhccchhhhccHHhhcC
Confidence 557789999999877655 6666654
No 198
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=25.75 E-value=37 Score=35.32 Aligned_cols=54 Identities=26% Similarity=0.500 Sum_probs=36.1
Q ss_pred CCCCcccCCCCCCCCCHH-HhhhhcccccCCCCCceecCCCcccc--hhhhhhhhhhcc
Q 028852 42 DVRPDFPCPYCYEDFDIA-SLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQH 97 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~-~L~~H~~~eH~~e~~~vVCPVCa~~v--s~d~i~Hl~~~H 97 (202)
..-..|+|+-|++-|-.. -|-+|+.- | ..-+..-||-|-.+. +..+-.||+..-
T Consensus 277 a~lRKFKCtECgKAFKfKHHLKEHlRI-H-SGEKPfeCpnCkKRFSHSGSySSHmSSKK 333 (1007)
T KOG3623|consen 277 ALLRKFKCTECGKAFKFKHHLKEHLRI-H-SGEKPFECPNCKKRFSHSGSYSSHMSSKK 333 (1007)
T ss_pred hhhccccccccchhhhhHHHHHhhhee-e-cCCCCcCCcccccccccCCcccccccccc
Confidence 445689999999966543 34444332 2 345678899999986 456777775543
No 199
>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=25.73 E-value=27 Score=27.35 Aligned_cols=19 Identities=21% Similarity=0.627 Sum_probs=12.9
Q ss_pred CcccCCCCCC-CCCHHHhhh
Q 028852 45 PDFPCPYCYE-DFDIASLCS 63 (202)
Q Consensus 45 ~~F~CPfC~e-~~dv~~L~~ 63 (202)
..|.||+|.. .=.+..+..
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~~ 42 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWVK 42 (178)
T ss_pred ECCCCcchhhhhHHHHHHHH
Confidence 4699999988 544544544
No 200
>PRK05978 hypothetical protein; Provisional
Probab=25.68 E-value=29 Score=28.81 Aligned_cols=28 Identities=25% Similarity=0.443 Sum_probs=17.0
Q ss_pred cccCCCCCC-CCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.-.||-|++ .+=. .+-.-+-.||+|-..
T Consensus 33 ~grCP~CG~G~LF~-----------g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 33 RGRCPACGEGKLFR-----------AFLKPVDHCAACGED 61 (148)
T ss_pred cCcCCCCCCCcccc-----------cccccCCCccccCCc
Confidence 368999999 4421 233334567777665
No 201
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.35 E-value=28 Score=27.58 Aligned_cols=13 Identities=15% Similarity=0.378 Sum_probs=7.6
Q ss_pred CCCcccCCCCCCCC
Q 028852 43 VRPDFPCPYCYEDF 56 (202)
Q Consensus 43 ~~~~F~CPfC~e~~ 56 (202)
.+..+.| -|+..|
T Consensus 67 vp~~~~C-~Cg~~~ 79 (124)
T PRK00762 67 IPVEIEC-ECGYEG 79 (124)
T ss_pred cCeeEEe-eCcCcc
Confidence 3556667 676543
No 202
>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=25.34 E-value=7 Score=30.14 Aligned_cols=21 Identities=29% Similarity=0.641 Sum_probs=16.5
Q ss_pred CcccCCCCCC-CCCHHHhhhhc
Q 028852 45 PDFPCPYCYE-DFDIASLCSHL 65 (202)
Q Consensus 45 ~~F~CPfC~e-~~dv~~L~~H~ 65 (202)
..|.||+|.. .-.+..|..+.
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 4699999988 77777888884
No 203
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=24.30 E-value=38 Score=25.71 Aligned_cols=37 Identities=27% Similarity=0.582 Sum_probs=26.8
Q ss_pred cccCCCCCC-----CCCHHHhhhhcccccCC------CCCceecCCCcc
Q 028852 46 DFPCPYCYE-----DFDIASLCSHLEDEHSC------ESKVTVCPICSV 83 (202)
Q Consensus 46 ~F~CPfC~e-----~~dv~~L~~H~~~eH~~------e~~~vVCPVCa~ 83 (202)
.=.||-|-. .+ +-++|.|+--.|+. ....+-||+|..
T Consensus 31 dg~Cp~Ck~PgDdCPL-v~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq 78 (84)
T KOG1493|consen 31 DGCCPDCKLPGDDCPL-VWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQ 78 (84)
T ss_pred CCcCCCCcCCCCCCcc-HHHHHHHHHHHHHHHHHhcCccccccCCcchh
Confidence 346888833 34 77899998888874 456688999964
No 204
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.14 E-value=45 Score=35.03 Aligned_cols=35 Identities=26% Similarity=0.335 Sum_probs=23.3
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
..+.||.|+..|....-- ...|.+..+.||.|.-.
T Consensus 249 ~~~~c~~~g~~~~~~~~~-----~FSfNsp~G~Cp~C~G~ 283 (924)
T TIGR00630 249 KHAACPECGFSLPELEPR-----LFSFNSPYGACPECSGL 283 (924)
T ss_pred hcccCcccCcccCcCChh-----hcCCCCCcCCCCCCccc
Confidence 469999999866532211 22456667999999554
No 205
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.00 E-value=38 Score=32.76 Aligned_cols=37 Identities=24% Similarity=0.446 Sum_probs=21.4
Q ss_pred cccCCCCCCCCC----HHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFD----IASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~d----v~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
...||.|+-.+. ...|.||--.. ...-+-.||-|...
T Consensus 222 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~--~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEGKLRCHYCGY--QEPIPKTCPQCGSE 262 (505)
T ss_pred ccCCCCCCCceEEecCCCeEEcCCCcC--cCCCCCCCCCCCCC
Confidence 456999986443 33555552221 12335689999764
No 206
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=23.95 E-value=74 Score=28.45 Aligned_cols=35 Identities=26% Similarity=0.407 Sum_probs=20.1
Q ss_pred CCCCcccCCCCCCCCCHHHhhhhcccccCCC--CCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCE--SKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e--~~~vVCPVCa~~v 85 (202)
......-||-|.- |-.-.|..+ ...-|||-|-+..
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 3455678998853 112223322 2247899998764
No 207
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=23.90 E-value=39 Score=28.08 Aligned_cols=11 Identities=27% Similarity=0.996 Sum_probs=8.6
Q ss_pred CceecCCCccc
Q 028852 74 KVTVCPICSVK 84 (202)
Q Consensus 74 ~~vVCPVCa~~ 84 (202)
.-+.||||-..
T Consensus 31 glv~CP~Cgs~ 41 (148)
T PF06676_consen 31 GLVSCPVCGST 41 (148)
T ss_pred CCccCCCCCCC
Confidence 45889999765
No 208
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=23.76 E-value=48 Score=28.09 Aligned_cols=40 Identities=20% Similarity=0.500 Sum_probs=26.5
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhh
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDM 89 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~ 89 (202)
....|..|+..+....+..++. +...-.||.|...+..++
T Consensus 108 ~~~~C~~C~~~~~~~~~~~~~~-----~~~~p~C~~Cg~~lrP~V 147 (218)
T cd01407 108 FRVRCTKCGKEYPRDELQADID-----REEVPRCPKCGGLLRPDV 147 (218)
T ss_pred CcceeCCCcCCCcHHHHhHhhc-----cCCCCcCCCCCCccCCCe
Confidence 4578999999877776653322 233457999987754444
No 209
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=23.69 E-value=45 Score=20.80 Aligned_cols=12 Identities=25% Similarity=0.562 Sum_probs=7.8
Q ss_pred CCCcccCCCCCC
Q 028852 43 VRPDFPCPYCYE 54 (202)
Q Consensus 43 ~~~~F~CPfC~e 54 (202)
......||+||-
T Consensus 14 ~~~~irC~~CG~ 25 (32)
T PF03604_consen 14 PGDPIRCPECGH 25 (32)
T ss_dssp TSSTSSBSSSS-
T ss_pred CCCcEECCcCCC
Confidence 345678888874
No 210
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.66 E-value=41 Score=26.83 Aligned_cols=15 Identities=40% Similarity=0.747 Sum_probs=12.2
Q ss_pred cccCCCCCCCCCHHH
Q 028852 46 DFPCPYCYEDFDIAS 60 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~ 60 (202)
...||-||+.|+-+-
T Consensus 49 ~t~CP~Cg~~~e~~f 63 (115)
T COG1885 49 STSCPKCGEPFESAF 63 (115)
T ss_pred cccCCCCCCccceeE
Confidence 678999999887543
No 211
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=23.60 E-value=63 Score=24.40 Aligned_cols=36 Identities=31% Similarity=0.537 Sum_probs=0.0
Q ss_pred CCCceecCCCcccc-hhhhhhhhhhcccchhhhhhhc
Q 028852 72 ESKVTVCPICSVKV-ARDMLSHITLQHGHLFKLQRRR 107 (202)
Q Consensus 72 e~~~vVCPVCa~~v-s~d~i~Hl~~~H~~~~k~~r~r 107 (202)
+.+.+||-.|-.-| ...+.+||..+|.......++.
T Consensus 8 ~~~vlIC~~C~~av~~~~v~~HL~~~H~~~~~~~~~~ 44 (109)
T PF12013_consen 8 EYRVLICRQCQYAVQPSEVESHLRKRHHILKSQERQR 44 (109)
T ss_pred cCCEEEeCCCCcccCchHHHHHHHHhcccccHHHHHH
No 212
>PHA02942 putative transposase; Provisional
Probab=23.51 E-value=60 Score=30.41 Aligned_cols=51 Identities=20% Similarity=0.365 Sum_probs=33.3
Q ss_pred cCCCcCCCCCCCCCcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhhhhhhh
Q 028852 32 LSIDDFEVEDDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITL 95 (202)
Q Consensus 32 ~~~~~~~~~dd~~~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i~Hl~~ 95 (202)
.|+.=+.++ ..-..=+||.||.-.- . ...+..+||-|-...-+|+.+-+++
T Consensus 312 ~G~~Vv~V~-p~yTSq~Cs~CG~~~~--~----------l~~r~f~C~~CG~~~drD~nAA~NI 362 (383)
T PHA02942 312 HGMIVEFVN-PSYSSVSCPKCGHKMV--E----------IAHRYFHCPSCGYENDRDVIAIMNL 362 (383)
T ss_pred hCCEEEEEC-CCCCCccCCCCCCccC--c----------CCCCEEECCCCCCEeCcHHHHHHHH
Confidence 355444443 2235678999997211 1 1235789999999988888887765
No 213
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=23.43 E-value=21 Score=32.66 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=5.8
Q ss_pred ceecCCCccc
Q 028852 75 VTVCPICSVK 84 (202)
Q Consensus 75 ~vVCPVCa~~ 84 (202)
.+.|+-|..+
T Consensus 266 ev~C~FC~~~ 275 (286)
T COG1281 266 EVTCEFCGTK 275 (286)
T ss_pred EEEeeccCCE
Confidence 4566666543
No 214
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=23.42 E-value=34 Score=29.30 Aligned_cols=27 Identities=33% Similarity=0.657 Sum_probs=18.3
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchh
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~ 87 (202)
..-.||-|| | +-...+.|+-|..+|..
T Consensus 92 nl~~CP~CG----------h------~k~a~~LC~~Cy~kV~k 118 (176)
T KOG4080|consen 92 NLNTCPACG----------H------IKPAHTLCDYCYAKVHK 118 (176)
T ss_pred ccccCcccC----------c------cccccccHHHHHHHHHH
Confidence 356899987 3 22345789999888743
No 215
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=23.26 E-value=36 Score=30.43 Aligned_cols=51 Identities=24% Similarity=0.504 Sum_probs=32.1
Q ss_pred cccCCCCCCCC-CHHHhhhhcccccCCCCCceecCCCcccch--hhhhhhhhhccc
Q 028852 46 DFPCPYCYEDF-DIASLCSHLEDEHSCESKVTVCPICSVKVA--RDMLSHITLQHG 98 (202)
Q Consensus 46 ~F~CPfC~e~~-dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs--~d~i~Hl~~~H~ 98 (202)
.+.|-|||++| |.-+|-.|.... ...++..|.+|..-.+ -.+-.|+.--||
T Consensus 145 r~lct~cgkgfndtfdlkrh~rth--tgvrpykc~~c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 145 RHLCTFCGKGFNDTFDLKRHTRTH--TGVRPYKCSLCEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred HHHHhhccCcccchhhhhhhhccc--cCccccchhhhhHHHHhhccHHHHHHHHcC
Confidence 47788888855 445677775554 4567778888866542 245666665444
No 216
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=23.21 E-value=35 Score=22.35 Aligned_cols=7 Identities=57% Similarity=1.554 Sum_probs=3.4
Q ss_pred cCCCCCC
Q 028852 48 PCPYCYE 54 (202)
Q Consensus 48 ~CPfC~e 54 (202)
+||.|+=
T Consensus 5 pCP~CGG 11 (40)
T PF08273_consen 5 PCPICGG 11 (40)
T ss_dssp --TTTT-
T ss_pred CCCCCcC
Confidence 7999954
No 217
>PRK02539 hypothetical protein; Provisional
Probab=23.19 E-value=77 Score=24.19 Aligned_cols=22 Identities=18% Similarity=0.412 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHHhcccchhhhHHHH
Q 028852 170 PSLSHEEREKRIRQGAGRASFVQDL 194 (202)
Q Consensus 170 ~~Ls~ee~eek~k~~~~r~eFVQgL 194 (202)
.-||.+|++|+.+ .|-+|++.+
T Consensus 19 ~gLT~eEk~Eq~~---LR~eYl~~f 40 (85)
T PRK02539 19 EGLTGEEKVEQAK---LREEYIEGY 40 (85)
T ss_pred cCCCHHHHHHHHH---HHHHHHHHH
Confidence 5799999988765 688877654
No 218
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.03 E-value=51 Score=33.28 Aligned_cols=39 Identities=18% Similarity=0.445 Sum_probs=24.5
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchh
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~ 87 (202)
.-.||.||..+.. .-|.+|-.+-+.+ ...||-|-..++.
T Consensus 15 akFC~~CG~~l~~-~~Cp~CG~~~~~~--~~fC~~CG~~~~~ 53 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQCGTEVPVD--EAHCPNCGAETGT 53 (645)
T ss_pred CccccccCCCCCC-CcCCCCCCCCCcc--cccccccCCcccc
Confidence 4568888776643 3466666664433 3478888887644
No 219
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=22.95 E-value=36 Score=28.35 Aligned_cols=31 Identities=19% Similarity=0.607 Sum_probs=18.1
Q ss_pred cCCCCCC-CCCHHHhhhhcccccCCCCCce-----ecCCCcccc
Q 028852 48 PCPYCYE-DFDIASLCSHLEDEHSCESKVT-----VCPICSVKV 85 (202)
Q Consensus 48 ~CPfC~e-~~dv~~L~~H~~~eH~~e~~~v-----VCPVCa~~v 85 (202)
.||||+. +--|. +. -..+..+. -|+-|..+.
T Consensus 2 ~CP~C~~~dtkVi------DS-R~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 2 HCPFCQHHNTRVL------DS-RLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCEee------ec-cccCCCCeeeecccCCccCCcc
Confidence 5999987 44332 22 22233333 399999874
No 220
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.89 E-value=51 Score=29.40 Aligned_cols=27 Identities=22% Similarity=0.534 Sum_probs=17.2
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICS 82 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa 82 (202)
-+||-||..+... --.......||.|-
T Consensus 255 ~pC~~Cg~~I~~~---------~~~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERI---------KLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEE---------EECCCccEECCCCc
Confidence 4899998653321 12346678899983
No 221
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=22.78 E-value=20 Score=36.57 Aligned_cols=46 Identities=20% Similarity=0.556 Sum_probs=32.3
Q ss_pred CCCcccCCCCCCCCC--HHHhhhhcccccC----CCCCceecCCCcccchhh
Q 028852 43 VRPDFPCPYCYEDFD--IASLCSHLEDEHS----CESKVTVCPICSVKVARD 88 (202)
Q Consensus 43 ~~~~F~CPfC~e~~d--v~~L~~H~~~eH~----~e~~~vVCPVCa~~vs~d 88 (202)
.+...+||.|....- +-..|-|+-=+-| ++++.-.||.|-+-.|.|
T Consensus 640 yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 640 YKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred HHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 367899999988443 3345667655544 367778899998877654
No 222
>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=22.64 E-value=47 Score=23.55 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=6.7
Q ss_pred cCCCCCCCCC
Q 028852 48 PCPYCYEDFD 57 (202)
Q Consensus 48 ~CPfC~e~~d 57 (202)
-||+||+.+.
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 4777777554
No 223
>PHA02540 61 DNA primase; Provisional
Probab=22.60 E-value=37 Score=31.60 Aligned_cols=10 Identities=40% Similarity=1.125 Sum_probs=8.7
Q ss_pred CcccCCCCCC
Q 028852 45 PDFPCPYCYE 54 (202)
Q Consensus 45 ~~F~CPfC~e 54 (202)
-.+.||||++
T Consensus 26 ~~~~CPf~~d 35 (337)
T PHA02540 26 YNFRCPICGD 35 (337)
T ss_pred EEecCCCCCC
Confidence 4789999998
No 224
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.58 E-value=27 Score=33.32 Aligned_cols=44 Identities=25% Similarity=0.543 Sum_probs=25.2
Q ss_pred CCCCcccCCCCCCCCCHH--HhhhhcccccCC---CCCceecCCCcccc
Q 028852 42 DVRPDFPCPYCYEDFDIA--SLCSHLEDEHSC---ESKVTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e~~dv~--~L~~H~~~eH~~---e~~~vVCPVCa~~v 85 (202)
++...|.||.|.+.|... .=|.|.-=..+. -.....||+|-..+
T Consensus 22 ~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~ 70 (397)
T TIGR00599 22 PLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAED 70 (397)
T ss_pred ccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCcc
Confidence 455689999998855443 234442211111 11234799998864
No 225
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=22.46 E-value=46 Score=31.95 Aligned_cols=10 Identities=30% Similarity=1.059 Sum_probs=7.6
Q ss_pred CCCcccCCCC
Q 028852 43 VRPDFPCPYC 52 (202)
Q Consensus 43 ~~~~F~CPfC 52 (202)
....|.|+.|
T Consensus 422 ~~~~~~c~~c 431 (479)
T PRK05452 422 LGPRMQCSVC 431 (479)
T ss_pred CCCeEEECCC
Confidence 3567888888
No 226
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=22.08 E-value=35 Score=24.44 Aligned_cols=9 Identities=33% Similarity=0.936 Sum_probs=6.0
Q ss_pred CCcccCCCC
Q 028852 44 RPDFPCPYC 52 (202)
Q Consensus 44 ~~~F~CPfC 52 (202)
-....||.|
T Consensus 6 LeiLaCP~~ 14 (60)
T COG2835 6 LEILACPVC 14 (60)
T ss_pred heeeeccCc
Confidence 346677777
No 227
>cd03024 DsbA_FrnE DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=22.02 E-value=22 Score=28.64 Aligned_cols=22 Identities=27% Similarity=0.671 Sum_probs=15.5
Q ss_pred CCcccCCCCCC-CCCHHHhhhhc
Q 028852 44 RPDFPCPYCYE-DFDIASLCSHL 65 (202)
Q Consensus 44 ~~~F~CPfC~e-~~dv~~L~~H~ 65 (202)
-..|.||||+. .-.+..+....
T Consensus 4 ~~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 4 WSDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred EecCcCccHHHHHHHHHHHHHhC
Confidence 45789999998 55666666554
No 228
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.84 E-value=54 Score=35.86 Aligned_cols=41 Identities=27% Similarity=0.505 Sum_probs=30.2
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccC-CCCCceecCCCcccc
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHS-CESKVTVCPICSVKV 85 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~-~e~~~vVCPVCa~~v 85 (202)
..+.||.||........|..|..+=. .++....||-|...+
T Consensus 678 ~~~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtpl 719 (1337)
T PRK14714 678 YENRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVEL 719 (1337)
T ss_pred ccccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCcc
Confidence 35799999997776778888877632 233467899998764
No 229
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.73 E-value=24 Score=26.64 Aligned_cols=46 Identities=22% Similarity=0.546 Sum_probs=31.0
Q ss_pred CcccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcccchhhhhhhhhhcccchhhh
Q 028852 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHGHLFKL 103 (202)
Q Consensus 45 ~~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~vs~d~i~Hl~~~H~~~~k~ 103 (202)
..|.|--|+..+|+. .|+ .+.-.+.||-|.+.+.+-| .+=|..||.
T Consensus 11 Y~Y~c~~cg~~~dvv---q~~-----~ddplt~ce~c~a~~kk~l-----~~vgi~fKG 56 (82)
T COG2331 11 YSYECTECGNRFDVV---QAM-----TDDPLTTCEECGARLKKLL-----NAVGIVFKG 56 (82)
T ss_pred eEEeecccchHHHHH---Hhc-----ccCccccChhhChHHHHhh-----ccceEEEec
Confidence 468999999987764 343 4456689999999765533 234455544
No 230
>PF04641 Rtf2: Rtf2 RING-finger
Probab=21.49 E-value=27 Score=30.75 Aligned_cols=44 Identities=27% Similarity=0.612 Sum_probs=27.2
Q ss_pred CCCCcccCCCCCCCCC----HHHh--hhhcccccCC-CCC-ceecCCCcccc
Q 028852 42 DVRPDFPCPYCYEDFD----IASL--CSHLEDEHSC-ESK-VTVCPICSVKV 85 (202)
Q Consensus 42 d~~~~F~CPfC~e~~d----v~~L--~~H~~~eH~~-e~~-~vVCPVCa~~v 85 (202)
.....|-||.++..|+ .+.| |-|+-.+=.. +.+ ...||||....
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f 160 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPF 160 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCcc
Confidence 3467899999988764 2222 3444443332 223 56799998863
No 231
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.49 E-value=47 Score=23.43 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=8.0
Q ss_pred cccCCCCCC
Q 028852 46 DFPCPYCYE 54 (202)
Q Consensus 46 ~F~CPfC~e 54 (202)
..+||||+.
T Consensus 35 ~~pC~fCg~ 43 (57)
T PF06221_consen 35 LGPCPFCGT 43 (57)
T ss_pred cCcCCCCCC
Confidence 679999997
No 232
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.97 E-value=23 Score=32.26 Aligned_cols=43 Identities=30% Similarity=0.643 Sum_probs=30.2
Q ss_pred CcccCCCCCC--CCCHHHhhhhcccccCC-----CCCceecCCCcccchh
Q 028852 45 PDFPCPYCYE--DFDIASLCSHLEDEHSC-----ESKVTVCPICSVKVAR 87 (202)
Q Consensus 45 ~~F~CPfC~e--~~dv~~L~~H~~~eH~~-----e~~~vVCPVCa~~vs~ 87 (202)
..|.|+.|-+ +.=.-..|-|+---|+. -.+...||+|.+++..
T Consensus 214 ~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred cccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 3789999988 44455667777666664 2345669999998643
No 233
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=20.79 E-value=41 Score=25.58 Aligned_cols=36 Identities=33% Similarity=0.594 Sum_probs=22.8
Q ss_pred cCCCCCC-CCC---HHHhhhhcccccCC------CCCceecCCCcc
Q 028852 48 PCPYCYE-DFD---IASLCSHLEDEHSC------ESKVTVCPICSV 83 (202)
Q Consensus 48 ~CPfC~e-~~d---v~~L~~H~~~eH~~------e~~~vVCPVCa~ 83 (202)
.||-|-. +-| +-+-|.|.--.|+. +..+..||+|..
T Consensus 34 ~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~ 79 (85)
T PF12861_consen 34 CCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQ 79 (85)
T ss_pred CCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCC
Confidence 3787765 434 22457776666653 345689999975
No 234
>PRK01546 hypothetical protein; Provisional
Probab=20.67 E-value=94 Score=23.37 Aligned_cols=22 Identities=23% Similarity=0.451 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHHhcccchhhhHHHH
Q 028852 170 PSLSHEEREKRIRQGAGRASFVQDL 194 (202)
Q Consensus 170 ~~Ls~ee~eek~k~~~~r~eFVQgL 194 (202)
.-||.+|++|+.+ .|-+|++.+
T Consensus 20 ~gLT~eEk~Eq~~---LR~eYl~~f 41 (79)
T PRK01546 20 EGLTEEEQRERQS---LREQYLKGF 41 (79)
T ss_pred cCCCHHHHHHHHH---HHHHHHHHH
Confidence 5699999988765 688877654
No 235
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.62 E-value=47 Score=30.64 Aligned_cols=10 Identities=30% Similarity=0.627 Sum_probs=7.8
Q ss_pred CcccCCCCCC
Q 028852 45 PDFPCPYCYE 54 (202)
Q Consensus 45 ~~F~CPfC~e 54 (202)
..=.||.||.
T Consensus 186 ~~~~CPvCGs 195 (309)
T PRK03564 186 QRQFCPVCGS 195 (309)
T ss_pred CCCCCCCCCC
Confidence 3567999987
No 236
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=20.62 E-value=53 Score=31.84 Aligned_cols=40 Identities=18% Similarity=0.496 Sum_probs=23.5
Q ss_pred CCcccCCCCCCCCCHHHhhh-----hcccccCCCCCceecCCCcc
Q 028852 44 RPDFPCPYCYEDFDIASLCS-----HLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 44 ~~~F~CPfC~e~~dv~~L~~-----H~~~eH~~e~~~vVCPVCa~ 83 (202)
|..|.||.|.-.+.+...-. .-............|+-|-=
T Consensus 50 r~Cf~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~W 94 (483)
T PF05502_consen 50 RNCFDCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRW 94 (483)
T ss_pred cccccCCCCCCcceeEecccccccccccccCCCCCEEEECCCcee
Confidence 46699999987666655443 11112223445678999943
No 237
>cd03021 DsbA_GSTK DsbA family, Glutathione (GSH) S-transferase Kappa (GSTK) subfamily; GSTK is a member of the GST family of enzymes which catalyzes the transfer of the thiol of GSH to electrophilic substrates. It is specifically located in the mitochondria and peroxisomes, unlike other members of the canonical GST family, which are mainly cytosolic. The biological substrates of GSTK are not yet known. It is presumed to have a protective role during respiration when large amounts of reactive oxygen species are generated. GSTK has the same general fold as DsbA, consisting of a thioredoxin domain interrupted by an alpha-helical domain and its biological unit is a homodimer. GSTK is closely related to the bacterial enzyme, 2-hydroxychromene-2-carboxylate (HCCA) isomerase. It shows little sequence similarity to the other members of the GST family.
Probab=20.48 E-value=17 Score=30.27 Aligned_cols=13 Identities=31% Similarity=0.518 Sum_probs=10.1
Q ss_pred CCCcccCCCCCCC
Q 028852 43 VRPDFPCPYCYED 55 (202)
Q Consensus 43 ~~~~F~CPfC~e~ 55 (202)
....|.||||+-+
T Consensus 5 ~~~D~vcPwcylg 17 (209)
T cd03021 5 LYYDVVSPYSYLA 17 (209)
T ss_pred EEEeCCChHHHHH
Confidence 3457999999874
No 238
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=20.39 E-value=44 Score=28.27 Aligned_cols=11 Identities=45% Similarity=1.256 Sum_probs=2.1
Q ss_pred CCCcccCCCCC
Q 028852 43 VRPDFPCPYCY 53 (202)
Q Consensus 43 ~~~~F~CPfC~ 53 (202)
.+..|.||||.
T Consensus 151 ~~~~~~Cp~C~ 161 (175)
T PF05280_consen 151 PRHSFVCPFCQ 161 (175)
T ss_dssp -SS----TT--
T ss_pred CCcCcCCCCCC
Confidence 34455566553
No 239
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=20.34 E-value=35 Score=25.66 Aligned_cols=10 Identities=40% Similarity=1.112 Sum_probs=8.3
Q ss_pred CcccCCCCCC
Q 028852 45 PDFPCPYCYE 54 (202)
Q Consensus 45 ~~F~CPfC~e 54 (202)
..|.||||..
T Consensus 13 ~D~~Cp~C~~ 22 (154)
T cd03023 13 FDYNCGYCKK 22 (154)
T ss_pred ECCCChhHHH
Confidence 3689999987
No 240
>PHA02776 E7 protein; Provisional
Probab=20.27 E-value=25 Score=27.52 Aligned_cols=38 Identities=26% Similarity=0.466 Sum_probs=23.6
Q ss_pred ccCCCCCCCCCHHHhhhhcccc----cCCCCCceecCCCccc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDE----HSCESKVTVCPICSVK 84 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~e----H~~e~~~vVCPVCa~~ 84 (202)
-.|..|+..+.+.-++.|-.-. =-.+.-..|||.|+.+
T Consensus 59 t~C~~C~~~lRL~V~st~~~IR~lqqLLl~~L~ivCp~Ca~~ 100 (101)
T PHA02776 59 TCCCGCDNNVRLVVECTEPDIQELHNLLLGSLNIVCPICAPK 100 (101)
T ss_pred eECCCCCCeEEEEEEcChhhHHHHHHHhcCCeEEECCCCCCC
Confidence 4688898876666555542111 0125667899999864
No 241
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=20.23 E-value=16 Score=26.48 Aligned_cols=32 Identities=22% Similarity=0.580 Sum_probs=18.6
Q ss_pred cccCCCCCC-CCCHHHhhhhcccccCCCCCc--eecCCCccc
Q 028852 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKV--TVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e-~~dv~~L~~H~~~eH~~e~~~--vVCPVCa~~ 84 (202)
.|+|.-|+. . .|.-..|.|+... +.||-|...
T Consensus 4 ~FTC~~C~~Rs-------~~~~sk~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 4 TFTCNKCGTRS-------AKMFSKQAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEEETTTTEEE-------EEEEEHHHHHTSEEEEE-TTS--E
T ss_pred EEEcCCCCCcc-------ceeeCHHHHhCCeEEEECCCCcce
Confidence 699999975 2 2444455555554 459999875
No 242
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=20.20 E-value=39 Score=26.49 Aligned_cols=36 Identities=25% Similarity=0.307 Sum_probs=27.8
Q ss_pred ccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCcc
Q 028852 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (202)
Q Consensus 47 F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~ 83 (202)
=.||.|+-.+.--.|+.-| ++-.|.+....|-||..
T Consensus 28 gkC~ICDS~VRP~tlVRiC-~eC~~Gs~q~~ciic~~ 63 (110)
T KOG1705|consen 28 GKCVICDSYVRPCTLVRIC-DECNYGSYQGRCVICGG 63 (110)
T ss_pred Ccccccccccccceeeeee-hhcCCccccCceEEecC
Confidence 4799998877777777644 45578888889999977
No 243
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.19 E-value=40 Score=30.52 Aligned_cols=8 Identities=25% Similarity=1.045 Sum_probs=5.5
Q ss_pred eecCCCcc
Q 028852 76 TVCPICSV 83 (202)
Q Consensus 76 vVCPVCa~ 83 (202)
..||+|.+
T Consensus 270 ~~C~~Cgt 277 (279)
T TIGR00627 270 PICKTCKT 277 (279)
T ss_pred CCCCCCCC
Confidence 47777765
No 244
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.02 E-value=59 Score=28.71 Aligned_cols=28 Identities=21% Similarity=0.512 Sum_probs=17.8
Q ss_pred cccCCCCCCCCCHHHhhhhcccccCCCCCceecCCCccc
Q 028852 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (202)
Q Consensus 46 ~F~CPfC~e~~dv~~L~~H~~~eH~~e~~~vVCPVCa~~ 84 (202)
.=.||+||..+... .+....+||-|...
T Consensus 99 ~~fC~~CG~~~~~~-----------~~~~~~~C~~c~~~ 126 (256)
T PRK00241 99 HRFCGYCGHPMHPS-----------KTEWAMLCPHCRER 126 (256)
T ss_pred CccccccCCCCeec-----------CCceeEECCCCCCE
Confidence 34799999855432 12345678888755
Done!