Query 030491
Match_columns 176
No_of_seqs 128 out of 184
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 14:31:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030491.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030491hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05605 zf-Di19: Drought indu 99.8 1.1E-20 2.5E-25 127.1 4.6 54 45-98 1-54 (54)
2 PF14571 Di19_C: Stress-induce 98.9 3.6E-10 7.9E-15 86.3 1.9 50 119-168 1-78 (105)
3 KOG1280 Uncharacterized conser 98.7 1.6E-08 3.5E-13 91.7 4.4 70 26-97 60-140 (381)
4 PF13894 zf-C2H2_4: C2H2-type 95.2 0.015 3.4E-07 31.2 1.9 23 47-69 1-24 (24)
5 COG5216 Uncharacterized conser 94.9 0.014 3.1E-07 41.8 1.4 35 42-85 18-54 (67)
6 KOG2923 Uncharacterized conser 94.8 0.02 4.3E-07 41.3 2.1 45 32-85 7-54 (67)
7 PF09237 GAGA: GAGA factor; I 94.7 0.025 5.3E-07 39.4 2.2 28 72-99 21-50 (54)
8 PF13913 zf-C2HC_2: zinc-finge 93.7 0.057 1.2E-06 31.5 2.1 21 46-66 2-22 (25)
9 PLN03086 PRLI-interacting fact 93.4 0.089 1.9E-06 50.9 4.1 49 44-97 451-500 (567)
10 PF00096 zf-C2H2: Zinc finger, 93.1 0.051 1.1E-06 29.8 1.2 21 47-67 1-22 (23)
11 PF12756 zf-C2H2_2: C2H2 type 92.4 0.09 2E-06 36.7 2.0 49 48-96 1-73 (100)
12 PHA00732 hypothetical protein 91.3 0.24 5.2E-06 36.2 3.2 42 47-93 2-44 (79)
13 PHA00733 hypothetical protein 91.0 0.37 7.9E-06 37.8 4.1 50 45-98 72-124 (128)
14 smart00531 TFIIE Transcription 90.6 0.24 5.1E-06 39.3 2.9 38 43-85 96-133 (147)
15 PF13909 zf-H2C2_5: C2H2-type 90.6 0.2 4.3E-06 27.9 1.8 24 47-70 1-24 (24)
16 PLN03086 PRLI-interacting fact 88.8 0.48 1E-05 46.0 3.9 37 46-85 478-514 (567)
17 KOG2462 C2H2-type Zn-finger pr 88.8 0.32 7E-06 43.5 2.5 37 44-84 159-196 (279)
18 PF08271 TF_Zn_Ribbon: TFIIB z 88.6 0.18 3.8E-06 32.4 0.6 33 47-89 1-33 (43)
19 PF14354 Lar_restr_allev: Rest 88.6 0.11 2.4E-06 34.9 -0.4 31 46-83 3-37 (61)
20 PRK09710 lar restriction allev 88.2 0.19 4.1E-06 36.1 0.5 30 46-84 6-36 (64)
21 TIGR01206 lysW lysine biosynth 87.6 0.18 4E-06 34.8 0.2 30 46-84 2-31 (54)
22 PHA02768 hypothetical protein; 87.6 0.5 1.1E-05 32.9 2.4 35 46-84 5-40 (55)
23 PLN03208 E3 ubiquitin-protein 87.0 0.28 6E-06 41.7 1.0 44 44-87 16-80 (193)
24 TIGR02098 MJ0042_CXXC MJ0042 f 86.6 0.53 1.2E-05 29.0 1.9 33 46-84 2-34 (38)
25 smart00834 CxxC_CXXC_SSSS Puta 86.3 0.15 3.2E-06 31.5 -0.7 32 45-84 4-35 (41)
26 KOG2462 C2H2-type Zn-finger pr 86.3 0.58 1.3E-05 41.9 2.7 47 46-94 187-236 (279)
27 PRK14892 putative transcriptio 84.8 0.37 7.9E-06 36.9 0.6 33 44-85 19-52 (99)
28 PF12756 zf-C2H2_2: C2H2 type 83.8 0.66 1.4E-05 32.3 1.5 26 45-70 49-75 (100)
29 PF09986 DUF2225: Uncharacteri 83.2 0.3 6.5E-06 41.1 -0.5 17 46-62 5-21 (214)
30 smart00734 ZnF_Rad18 Rad18-lik 81.8 1.3 2.9E-05 26.1 2.0 20 47-66 2-21 (26)
31 KOG1842 FYVE finger-containing 80.3 1 2.3E-05 43.0 1.9 33 42-74 11-44 (505)
32 TIGR02605 CxxC_CxxC_SSSS putat 80.0 0.74 1.6E-05 30.0 0.6 31 45-83 4-34 (52)
33 PHA00616 hypothetical protein 79.7 1.1 2.5E-05 29.8 1.4 26 47-72 2-28 (44)
34 PF02176 zf-TRAF: TRAF-type zi 79.7 0.62 1.3E-05 30.7 0.2 45 46-92 9-60 (60)
35 KOG3623 Homeobox transcription 79.6 0.75 1.6E-05 46.5 0.7 51 44-94 208-261 (1007)
36 smart00504 Ubox Modified RING 79.3 2.1 4.6E-05 28.1 2.7 27 53-86 20-46 (63)
37 PF14255 Cys_rich_CPXG: Cystei 78.9 0.57 1.2E-05 32.1 -0.2 12 47-58 1-12 (52)
38 smart00355 ZnF_C2H2 zinc finge 78.1 2.9 6.2E-05 22.0 2.5 22 47-69 1-23 (26)
39 PRK14890 putative Zn-ribbon RN 77.2 2 4.3E-05 30.5 2.1 32 44-82 23-55 (59)
40 PF13912 zf-C2H2_6: C2H2-type 77.2 1.4 3E-05 24.8 1.1 24 46-69 1-25 (27)
41 PF08274 PhnA_Zn_Ribbon: PhnA 76.7 0.82 1.8E-05 28.2 0.1 24 48-83 4-27 (30)
42 PF05129 Elf1: Transcription e 76.6 1.1 2.3E-05 32.9 0.7 34 44-84 20-55 (81)
43 PF03470 zf-XS: XS zinc finger 76.5 1.8 4E-05 28.8 1.7 9 56-64 12-20 (43)
44 PF14206 Cys_rich_CPCC: Cystei 76.4 1.1 2.4E-05 33.1 0.7 27 46-83 1-28 (78)
45 PRK00398 rpoP DNA-directed RNA 76.4 1.5 3.2E-05 28.3 1.2 28 46-84 3-30 (46)
46 PTZ00255 60S ribosomal protein 75.6 0.83 1.8E-05 34.7 -0.2 34 40-85 30-64 (90)
47 cd00350 rubredoxin_like Rubred 75.6 0.98 2.1E-05 27.6 0.2 24 47-83 2-25 (33)
48 PF05605 zf-Di19: Drought indu 75.5 2.4 5.3E-05 28.1 2.1 24 46-70 31-54 (54)
49 KOG2932 E3 ubiquitin ligase in 75.5 1.7 3.7E-05 40.2 1.7 58 46-103 90-177 (389)
50 COG1655 Uncharacterized protei 74.8 1.2 2.6E-05 39.5 0.6 12 45-56 18-29 (267)
51 KOG2593 Transcription initiati 74.6 2 4.3E-05 40.7 2.0 98 34-138 116-236 (436)
52 COG5236 Uncharacterized conser 74.6 2.9 6.3E-05 39.3 3.0 55 44-104 218-312 (493)
53 PF03145 Sina: Seven in absent 73.5 2.2 4.8E-05 34.8 1.8 54 45-101 13-75 (198)
54 TIGR03655 anti_R_Lar restricti 71.1 1.8 3.9E-05 28.9 0.6 30 48-84 3-35 (53)
55 cd00729 rubredoxin_SM Rubredox 70.3 1.5 3.3E-05 27.2 0.2 26 46-84 2-27 (34)
56 TIGR00280 L37a ribosomal prote 70.2 1.2 2.6E-05 33.9 -0.4 17 40-56 29-46 (91)
57 TIGR00373 conserved hypothetic 69.3 5.7 0.00012 32.0 3.3 33 43-85 106-138 (158)
58 PRK06266 transcription initiat 69.0 3.7 8E-05 33.9 2.2 33 43-85 114-146 (178)
59 PRK03976 rpl37ae 50S ribosomal 68.4 1.4 3.1E-05 33.4 -0.3 17 40-56 30-47 (90)
60 PF04564 U-box: U-box domain; 68.2 5.3 0.00011 28.0 2.6 36 44-85 2-49 (73)
61 PF07754 DUF1610: Domain of un 67.7 3.1 6.6E-05 24.6 1.1 11 44-54 14-24 (24)
62 PF12773 DZR: Double zinc ribb 67.1 3 6.4E-05 26.9 1.0 28 47-86 13-40 (50)
63 PF04780 DUF629: Protein of un 66.6 5.1 0.00011 38.2 2.8 41 44-84 55-99 (466)
64 PRK12495 hypothetical protein; 66.4 3.8 8.2E-05 35.8 1.8 29 45-86 41-69 (226)
65 COG4888 Uncharacterized Zn rib 65.6 2.9 6.2E-05 32.7 0.8 36 44-84 20-55 (104)
66 COG2888 Predicted Zn-ribbon RN 64.8 6 0.00013 28.3 2.2 34 42-82 23-57 (61)
67 PF13395 HNH_4: HNH endonuclea 64.6 3.7 8.1E-05 27.4 1.1 14 49-62 1-14 (54)
68 KOG0320 Predicted E3 ubiquitin 63.5 5 0.00011 34.2 2.0 43 45-87 130-179 (187)
69 smart00659 RPOLCX RNA polymera 63.1 4.3 9.2E-05 26.7 1.2 28 46-85 2-29 (44)
70 PF11789 zf-Nse: Zinc-finger o 62.7 6.3 0.00014 27.0 2.0 33 43-80 8-53 (57)
71 PF15616 TerY-C: TerY-C metal 62.6 2.1 4.5E-05 34.4 -0.5 39 47-87 78-117 (131)
72 COG1592 Rubrerythrin [Energy p 62.4 4.8 0.0001 33.5 1.7 25 46-84 134-158 (166)
73 COG0675 Transposase and inacti 62.1 7.7 0.00017 32.1 2.8 46 33-94 296-341 (364)
74 PRK00420 hypothetical protein; 60.8 6.1 0.00013 31.0 1.9 27 47-85 24-50 (112)
75 PF09723 Zn-ribbon_8: Zinc rib 58.5 2.5 5.5E-05 27.1 -0.5 31 45-83 4-34 (42)
76 PF07282 OrfB_Zn_ribbon: Putat 58.1 11 0.00024 25.6 2.7 47 32-91 15-62 (69)
77 COG4311 SoxD Sarcosine oxidase 58.0 4.6 9.9E-05 31.2 0.7 9 46-54 3-11 (97)
78 TIGR00100 hypA hydrogenase nic 57.0 3 6.5E-05 32.0 -0.4 30 42-84 66-95 (115)
79 PF13465 zf-H2C2_2: Zinc-finge 56.5 10 0.00022 21.7 1.9 23 60-84 1-23 (26)
80 COG5175 MOT2 Transcriptional r 56.4 7.4 0.00016 36.6 1.9 35 49-84 17-62 (480)
81 PF10571 UPF0547: Uncharacteri 55.8 6.9 0.00015 23.2 1.1 8 49-56 3-10 (26)
82 PF08996 zf-DNA_Pol: DNA Polym 55.6 2 4.4E-05 35.4 -1.7 40 44-85 16-55 (188)
83 PF14634 zf-RING_5: zinc-RING 55.4 9.1 0.0002 24.2 1.7 20 61-82 24-43 (44)
84 PF01780 Ribosomal_L37ae: Ribo 54.4 5.1 0.00011 30.4 0.5 13 42-54 31-43 (90)
85 PF09538 FYDLN_acid: Protein o 54.2 10 0.00022 29.3 2.1 33 42-87 5-38 (108)
86 PF14616 DUF4451: Domain of un 54.2 8.6 0.00019 30.1 1.7 28 75-102 25-57 (124)
87 PF04981 NMD3: NMD3 family ; 54.2 8.7 0.00019 32.5 1.9 36 49-84 1-44 (236)
88 PF14446 Prok-RING_1: Prokaryo 53.3 10 0.00022 26.4 1.8 25 47-84 6-30 (54)
89 PRK12496 hypothetical protein; 53.1 9.3 0.0002 31.1 1.8 28 46-86 127-154 (164)
90 cd00730 rubredoxin Rubredoxin; 52.9 7.1 0.00015 26.4 0.9 13 42-54 30-42 (50)
91 PRK03922 hypothetical protein; 52.4 7 0.00015 30.9 1.0 14 46-59 49-62 (113)
92 PF13719 zinc_ribbon_5: zinc-r 52.4 16 0.00034 22.8 2.4 30 47-84 3-34 (37)
93 smart00451 ZnF_U1 U1-like zinc 52.1 12 0.00026 21.9 1.8 22 46-67 3-25 (35)
94 COG5189 SFP1 Putative transcri 51.9 7.6 0.00016 36.2 1.3 40 46-85 349-408 (423)
95 PF04475 DUF555: Protein of un 51.2 7.5 0.00016 30.3 1.0 14 46-59 47-60 (102)
96 PF12171 zf-C2H2_jaz: Zinc-fin 51.1 9.4 0.0002 21.8 1.2 21 47-67 2-23 (27)
97 PF10058 DUF2296: Predicted in 50.7 7.4 0.00016 26.6 0.8 9 46-54 44-52 (54)
98 PRK11088 rrmA 23S rRNA methylt 49.3 3.8 8.3E-05 34.7 -1.0 28 46-73 2-29 (272)
99 TIGR00570 cdk7 CDK-activating 48.7 10 0.00022 34.5 1.5 38 46-84 3-52 (309)
100 PF00301 Rubredoxin: Rubredoxi 47.8 9.2 0.0002 25.6 0.9 13 42-54 30-42 (47)
101 PF04423 Rad50_zn_hook: Rad50 47.4 7.4 0.00016 25.8 0.4 14 48-61 22-35 (54)
102 smart00507 HNHc HNH nucleases. 47.2 3.1 6.7E-05 25.3 -1.4 21 47-67 11-31 (52)
103 PF13248 zf-ribbon_3: zinc-rib 46.8 12 0.00026 21.6 1.2 8 48-55 4-11 (26)
104 KOG0402 60S ribosomal protein 46.7 5.9 0.00013 30.2 -0.2 13 42-54 32-44 (92)
105 PRK12380 hydrogenase nickel in 46.2 6.4 0.00014 30.2 -0.1 30 42-84 66-95 (113)
106 smart00661 RPOL9 RNA polymeras 45.8 9.6 0.00021 24.4 0.7 10 75-84 20-29 (52)
107 PRK11595 DNA utilization prote 45.8 10 0.00022 31.7 1.1 21 48-68 7-29 (227)
108 COG1499 NMD3 NMD protein affec 45.7 12 0.00027 34.4 1.6 41 44-84 4-52 (355)
109 KOG2177 Predicted E3 ubiquitin 45.4 7.8 0.00017 30.3 0.3 36 45-82 12-54 (386)
110 PF08209 Sgf11: Sgf11 (transcr 45.2 20 0.00044 22.4 2.1 21 74-94 3-24 (33)
111 COG1997 RPL43A Ribosomal prote 44.9 4.6 0.0001 30.8 -1.0 35 39-84 28-62 (89)
112 COG4049 Uncharacterized protei 44.6 11 0.00024 26.9 0.9 26 76-101 18-45 (65)
113 PF02892 zf-BED: BED zinc fing 44.4 20 0.00043 22.3 2.0 24 74-97 15-44 (45)
114 PF04780 DUF629: Protein of un 43.6 12 0.00027 35.7 1.3 48 55-102 20-86 (466)
115 PF12760 Zn_Tnp_IS1595: Transp 43.5 13 0.00029 24.0 1.1 10 45-54 17-26 (46)
116 PF13824 zf-Mss51: Zinc-finger 42.2 13 0.00028 26.0 0.9 11 44-54 12-22 (55)
117 PF14353 CpXC: CpXC protein 42.0 12 0.00025 28.5 0.8 30 44-77 36-65 (128)
118 KOG3576 Ovo and related transc 42.0 15 0.00032 32.5 1.5 51 47-99 146-199 (267)
119 PF11672 DUF3268: Protein of u 41.8 11 0.00023 29.1 0.6 38 47-87 3-43 (102)
120 PF00097 zf-C3HC4: Zinc finger 41.4 2.4 5.2E-05 25.9 -2.6 9 73-81 33-41 (41)
121 KOG3608 Zn finger proteins [Ge 41.3 32 0.00069 32.7 3.6 48 46-94 263-313 (467)
122 smart00614 ZnF_BED BED zinc fi 41.3 16 0.00035 23.8 1.2 26 45-70 17-48 (50)
123 PRK03824 hypA hydrogenase nick 41.0 8.6 0.00019 30.4 -0.1 18 42-59 66-83 (135)
124 PHA00733 hypothetical protein 40.2 28 0.0006 27.3 2.6 25 46-70 99-124 (128)
125 TIGR00373 conserved hypothetic 40.0 20 0.00043 28.9 1.8 21 45-65 127-150 (158)
126 cd03019 DsbA_DsbA DsbA family, 39.5 12 0.00025 28.6 0.4 19 45-63 23-42 (178)
127 COG4049 Uncharacterized protei 39.2 12 0.00025 26.9 0.3 26 46-71 17-43 (65)
128 PF02146 SIR2: Sir2 family; I 39.0 12 0.00025 29.9 0.4 41 45-90 104-144 (178)
129 PF12660 zf-TFIIIC: Putative z 39.0 6.2 0.00013 29.7 -1.1 38 48-85 16-65 (99)
130 PF01155 HypA: Hydrogenase exp 38.9 4.3 9.3E-05 31.0 -2.1 29 43-84 67-95 (113)
131 PRK00423 tfb transcription ini 38.7 18 0.0004 31.9 1.6 37 45-92 10-47 (310)
132 KOG3608 Zn finger proteins [Ge 38.7 26 0.00056 33.3 2.6 43 59-101 335-380 (467)
133 PF03966 Trm112p: Trm112p-like 38.7 21 0.00046 24.7 1.6 39 45-83 6-61 (68)
134 PF14447 Prok-RING_4: Prokaryo 38.5 16 0.00034 25.6 0.9 13 46-58 39-51 (55)
135 PF13717 zinc_ribbon_4: zinc-r 38.3 32 0.00068 21.5 2.2 31 47-83 3-33 (36)
136 PRK05477 gatB aspartyl/glutamy 37.1 12 0.00026 35.6 0.2 17 70-86 32-48 (474)
137 TIGR00686 phnA alkylphosphonat 37.1 15 0.00033 28.9 0.7 12 73-84 17-28 (109)
138 TIGR01374 soxD sarcosine oxida 37.1 15 0.00033 27.6 0.7 8 47-54 2-9 (84)
139 PF12230 PRP21_like_P: Pre-mRN 36.7 12 0.00025 31.5 0.0 38 75-112 168-207 (229)
140 COG1675 TFA1 Transcription ini 36.3 17 0.00037 30.5 1.0 30 44-85 111-142 (176)
141 PF12230 PRP21_like_P: Pre-mRN 36.3 12 0.00026 31.4 0.0 23 46-68 168-190 (229)
142 TIGR02300 FYDLN_acid conserved 36.2 24 0.00053 28.5 1.8 32 42-86 5-37 (129)
143 PF14968 CCDC84: Coiled coil p 35.8 19 0.0004 33.1 1.2 18 42-59 54-71 (336)
144 PRK04023 DNA polymerase II lar 35.8 15 0.00033 38.5 0.7 36 46-85 638-673 (1121)
145 PF09706 Cas_CXXC_CXXC: CRISPR 35.6 13 0.00028 26.4 0.1 11 44-54 3-13 (69)
146 COG4391 Uncharacterized protei 35.3 20 0.00043 25.7 1.0 13 72-84 45-57 (62)
147 PRK06266 transcription initiat 34.1 28 0.00061 28.7 1.9 19 45-63 135-156 (178)
148 PF13462 Thioredoxin_4: Thiore 33.7 3.7 8.1E-05 30.8 -3.1 21 45-65 20-41 (162)
149 KOG2817 Predicted E3 ubiquitin 33.6 23 0.0005 33.3 1.4 16 44-59 372-387 (394)
150 KOG1493 Anaphase-promoting com 33.6 34 0.00074 25.8 2.0 36 47-83 32-78 (84)
151 PF12874 zf-met: Zinc-finger o 33.4 25 0.00054 19.2 1.0 16 78-93 3-20 (25)
152 KOG0823 Predicted E3 ubiquitin 33.3 13 0.00029 32.6 -0.2 43 44-87 45-96 (230)
153 KOG2879 Predicted E3 ubiquitin 33.0 13 0.00028 33.8 -0.3 41 45-85 238-286 (298)
154 PLN02751 glutamyl-tRNA(Gln) am 32.8 15 0.00033 35.6 0.2 20 67-86 85-104 (544)
155 PRK00564 hypA hydrogenase nick 32.3 14 0.00031 28.4 -0.1 31 42-84 67-97 (117)
156 PF05207 zf-CSL: CSL zinc fing 32.2 17 0.00037 24.7 0.3 44 34-86 5-51 (55)
157 KOG4628 Predicted E3 ubiquitin 31.9 9.6 0.00021 35.2 -1.3 40 46-85 229-277 (348)
158 PF09862 DUF2089: Protein of u 31.5 8.9 0.00019 30.1 -1.4 22 49-85 1-22 (113)
159 PF11290 DUF3090: Protein of u 31.5 24 0.00053 29.7 1.1 13 47-59 155-167 (171)
160 PF04267 SoxD: Sarcosine oxida 31.2 12 0.00027 28.0 -0.6 7 48-54 3-9 (84)
161 PF10276 zf-CHCC: Zinc-finger 30.9 19 0.0004 23.5 0.2 9 46-54 29-37 (40)
162 cd02972 DsbA_family DsbA famil 30.8 13 0.00029 24.5 -0.5 17 46-62 6-23 (98)
163 COG1656 Uncharacterized conser 30.6 38 0.00082 28.4 2.1 38 47-84 98-139 (165)
164 PF14369 zf-RING_3: zinc-finge 30.5 24 0.00052 22.1 0.7 9 48-56 23-31 (35)
165 PHA02929 N1R/p28-like protein; 30.4 10 0.00022 33.1 -1.3 41 45-85 173-226 (238)
166 KOG3576 Ovo and related transc 30.3 32 0.0007 30.5 1.7 55 46-100 173-239 (267)
167 KOG2231 Predicted E3 ubiquitin 30.1 34 0.00075 34.2 2.0 28 44-71 180-208 (669)
168 TIGR00133 gatB glutamyl-tRNA(G 30.0 19 0.0004 34.4 0.2 15 72-86 34-48 (478)
169 PRK14714 DNA polymerase II lar 29.9 20 0.00043 38.4 0.4 35 46-85 667-702 (1337)
170 COG3058 FdhE Uncharacterized p 29.8 17 0.00037 33.1 -0.1 18 74-91 184-201 (308)
171 TIGR03830 CxxCG_CxxCG_HTH puta 29.8 13 0.00028 27.6 -0.7 37 49-85 1-41 (127)
172 PF05876 Terminase_GpA: Phage 29.6 24 0.00053 33.8 0.9 42 44-87 198-241 (557)
173 PF11793 FANCL_C: FANCL C-term 28.5 35 0.00077 23.9 1.4 44 43-86 17-66 (70)
174 KOG4696 Uncharacterized conser 28.3 37 0.0008 31.6 1.8 24 46-70 2-25 (393)
175 PRK09678 DNA-binding transcrip 28.3 27 0.00059 25.3 0.8 8 47-54 2-9 (72)
176 PF06957 COPI_C: Coatomer (COP 28.1 17 0.00036 34.3 -0.5 32 45-89 379-411 (422)
177 PF09334 tRNA-synt_1g: tRNA sy 27.9 14 0.0003 33.8 -1.0 39 47-85 137-176 (391)
178 KOG1074 Transcriptional repres 27.9 21 0.00046 36.8 0.2 49 47-97 354-405 (958)
179 PRK10220 hypothetical protein; 27.5 42 0.00091 26.5 1.7 10 74-83 19-28 (111)
180 COG5109 Uncharacterized conser 27.3 27 0.00058 32.6 0.7 11 44-54 374-384 (396)
181 PRK03681 hypA hydrogenase nick 27.2 19 0.00041 27.7 -0.2 11 44-54 68-78 (114)
182 PF03604 DNA_RNApol_7kD: DNA d 26.9 37 0.00081 21.0 1.1 12 43-54 14-25 (32)
183 PHA02565 49 recombination endo 26.6 21 0.00045 29.8 -0.1 40 46-85 20-65 (157)
184 PHA02540 61 DNA primase; Provi 26.1 29 0.00064 31.7 0.8 24 78-103 58-81 (337)
185 PF13453 zf-TFIIB: Transcripti 26.0 20 0.00043 22.6 -0.3 9 49-57 2-10 (41)
186 cd03024 DsbA_FrnE DsbA family, 25.6 17 0.00036 28.6 -0.8 22 44-65 4-26 (201)
187 PF09889 DUF2116: Uncharacteri 25.6 46 0.001 23.3 1.5 10 48-57 5-14 (59)
188 KOG3940 Uncharacterized conser 25.5 42 0.00091 31.1 1.6 23 42-64 16-38 (351)
189 COG1405 SUA7 Transcription ini 25.3 39 0.00085 30.1 1.4 43 47-99 2-44 (285)
190 KOG3623 Homeobox transcription 25.0 42 0.0009 34.6 1.6 53 43-97 278-333 (1007)
191 PRK05452 anaerobic nitric oxid 25.0 40 0.00086 31.6 1.4 12 43-54 422-433 (479)
192 PF02934 GatB_N: GatB/GatE cat 24.9 20 0.00043 32.3 -0.5 19 68-86 25-43 (289)
193 PRK00464 nrdR transcriptional 24.8 32 0.00069 28.1 0.7 32 48-85 2-38 (154)
194 KOG1002 Nucleotide excision re 24.7 41 0.00088 33.6 1.5 55 39-93 529-593 (791)
195 PF12013 DUF3505: Protein of u 24.7 60 0.0013 24.0 2.1 30 71-100 7-37 (109)
196 cd03023 DsbA_Com1_like DsbA fa 24.3 25 0.00054 25.7 -0.0 9 46-54 14-22 (154)
197 TIGR00599 rad18 DNA repair pro 24.3 41 0.00088 31.5 1.3 18 76-93 182-200 (397)
198 PF04551 GcpE: GcpE protein; 23.9 40 0.00087 31.4 1.2 81 46-129 268-357 (359)
199 cd03021 DsbA_GSTK DsbA family, 23.3 13 0.00029 30.1 -1.8 13 43-55 5-17 (209)
200 PF07191 zinc-ribbons_6: zinc- 23.3 5 0.00011 29.3 -3.8 38 48-85 3-40 (70)
201 PF06677 Auto_anti-p27: Sjogre 23.3 51 0.0011 21.4 1.3 23 48-82 19-41 (41)
202 PRK00762 hypA hydrogenase nick 23.2 26 0.00055 27.3 -0.2 11 47-57 93-104 (124)
203 PRK00241 nudC NADH pyrophospha 22.9 46 0.001 28.8 1.3 27 47-84 100-126 (256)
204 PF05280 FlhC: Flagellar trans 22.7 37 0.0008 28.2 0.7 12 42-53 150-161 (175)
205 COG1198 PriA Primosomal protei 22.6 28 0.00061 35.0 -0.1 41 42-84 440-484 (730)
206 COG1645 Uncharacterized Zn-fin 22.6 37 0.0008 27.5 0.6 26 46-84 28-53 (131)
207 PF09779 Ima1_N: Ima1 N-termin 22.4 42 0.00091 26.3 0.9 17 45-61 19-37 (131)
208 COG1885 Uncharacterized protei 22.3 43 0.00094 26.5 0.9 14 46-59 49-62 (115)
209 TIGR00244 transcriptional regu 22.2 37 0.00081 27.9 0.6 31 48-85 2-38 (147)
210 PF12861 zf-Apc11: Anaphase-pr 22.1 38 0.00083 25.5 0.6 37 48-84 34-80 (85)
211 PF04810 zf-Sec23_Sec24: Sec23 21.7 36 0.00079 21.5 0.4 11 44-54 22-32 (40)
212 COG1281 Disulfide bond chapero 21.6 51 0.0011 29.8 1.4 30 32-61 250-283 (286)
213 PRK11639 zinc uptake transcrip 21.6 75 0.0016 25.6 2.2 40 46-85 100-150 (169)
214 PF06221 zf-C2HC5: Putative zi 21.6 46 0.001 23.2 0.9 9 46-54 35-43 (57)
215 CHL00174 accD acetyl-CoA carbo 21.4 54 0.0012 29.6 1.5 29 46-84 38-66 (296)
216 PF14279 HNH_5: HNH endonuclea 21.2 34 0.00075 24.4 0.2 40 49-89 1-44 (71)
217 KOG3214 Uncharacterized Zn rib 21.1 38 0.00081 26.7 0.4 36 44-84 21-56 (109)
218 PF08273 Prim_Zn_Ribbon: Zinc- 21.1 41 0.00089 21.8 0.5 7 48-54 5-11 (40)
219 PF12013 DUF3505: Protein of u 21.0 75 0.0016 23.5 2.0 26 45-70 79-109 (109)
220 cd03022 DsbA_HCCA_Iso DsbA fam 21.0 17 0.00038 28.1 -1.5 20 44-63 4-24 (192)
221 PRK05978 hypothetical protein; 20.9 27 0.00058 28.6 -0.5 28 46-84 33-61 (148)
222 PF13240 zinc_ribbon_2: zinc-r 20.8 41 0.00088 19.2 0.4 6 49-54 2-7 (23)
223 KOG4727 U1-like Zn-finger prot 20.5 45 0.00097 28.6 0.7 19 77-95 77-97 (193)
224 KOG1734 Predicted RING-contain 20.2 30 0.00066 31.6 -0.3 17 47-63 271-287 (328)
225 TIGR00612 ispG_gcpE 1-hydroxy- 20.1 83 0.0018 29.3 2.4 27 45-71 258-285 (346)
226 COG1773 Rubredoxin [Energy pro 20.1 54 0.0012 22.9 1.0 14 41-54 31-44 (55)
227 TIGR00515 accD acetyl-CoA carb 20.1 64 0.0014 28.7 1.7 29 46-84 26-54 (285)
228 cd01407 SIR2-fam SIR2 family o 20.1 66 0.0014 26.6 1.7 36 45-85 108-143 (218)
No 1
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=99.82 E-value=1.1e-20 Score=127.08 Aligned_cols=54 Identities=48% Similarity=0.938 Sum_probs=52.1
Q ss_pred CcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccchhhHHHHhhhhcc
Q 030491 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHG 98 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~d~l~HL~~rH~ 98 (176)
++|+||||+++||+.+|++|++++|+.+.++||||||+.+++.||++||+.+|+
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 379999999999999999999999999999999999999999999999999996
No 2
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=98.93 E-value=3.6e-10 Score=86.34 Aligned_cols=50 Identities=46% Similarity=0.518 Sum_probs=43.2
Q ss_pred hHhhhhhhhhhhhhHHHhcc----------------------------cchhhcccccccccccccccCCcCCccccc
Q 030491 119 ALSLLGRDLREAHLQVLLGE----------------------------AEEISKSVVTSTEDTSAKSAAPTHMWKTRY 168 (176)
Q Consensus 119 ~ls~l~kelre~~lq~llg~----------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 168 (176)
|||||||||||||||+|||| +++++|+..++.++++.++..+.+.|+++.
T Consensus 1 tlsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~s~ 78 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSEEKKSSKKSSSEQNVKSSA 78 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCccccccCCccccccccccccccchhccccccc
Confidence 68999999999999999994 356677777888899999999999998654
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.68 E-value=1.6e-08 Score=91.66 Aligned_cols=70 Identities=21% Similarity=0.466 Sum_probs=56.6
Q ss_pred cccccc-cCCCCCCCCCCCCCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccc---------hhhHHHHhh
Q 030491 26 SSQIDR-LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV---------ARDMLSHIT 94 (176)
Q Consensus 26 rs~~d~-~g~d~~~~ddd~r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~---------s~d~l~HL~ 94 (176)
|-++++ ||+|-+..+++. .|+||||++ +|.+..+.+|+...|+.-...+|||||++.+ ..+...|+.
T Consensus 60 ~~dfeL~f~Ge~i~~y~~q--SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~~qp~~~~~~~~~~~~~~ 137 (381)
T KOG1280|consen 60 RVDFELYFGGEPISHYDPQ--SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPEMQPIHSKETENLSVHWT 137 (381)
T ss_pred ccceeeEecCccccccccc--cccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcccCchhhhhhhhhhhhhh
Confidence 356665 788877775544 999999999 9999999999999999999999999999986 335555555
Q ss_pred hhc
Q 030491 95 LQH 97 (176)
Q Consensus 95 ~rH 97 (176)
..|
T Consensus 138 ~~a 140 (381)
T KOG1280|consen 138 EIA 140 (381)
T ss_pred hhc
Confidence 444
No 4
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=95.20 E-value=0.015 Score=31.21 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=17.3
Q ss_pred ccCCCCCC-CCCHHHHHhhhhhhc
Q 030491 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (176)
Q Consensus 47 F~CPFC~e-~fDv~~L~~H~~eeH 69 (176)
|.||+|+. --+..+|..|+...|
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 68999988 777888888888766
No 5
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.85 E-value=0.014 Score=41.79 Aligned_cols=35 Identities=31% Similarity=0.765 Sum_probs=25.7
Q ss_pred CCCCcccCCCCCC--CCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 42 DVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 42 d~r~~F~CPFC~e--~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
+..-+|+|| ||. ++....|. ..-..++||-|+-++
T Consensus 18 ~~~ftyPCP-CGDRFeIsLeDl~--------~GE~VArCPSCSLiv 54 (67)
T COG5216 18 EKTFTYPCP-CGDRFEISLEDLR--------NGEVVARCPSCSLIV 54 (67)
T ss_pred CceEEecCC-CCCEeEEEHHHhh--------CCceEEEcCCceEEE
Confidence 445789999 888 55555553 345678999999876
No 6
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.82 E-value=0.02 Score=41.35 Aligned_cols=45 Identities=33% Similarity=0.762 Sum_probs=30.3
Q ss_pred cCCCCCC-CCCCCCCcccCCCCCCC--CCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 32 LSIDDFE-VEDDVRPDFPCPYCYED--FDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 32 ~g~d~~~-~ddd~r~~F~CPFC~e~--fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
..++|++ .+|...-+|+|| ||.. +....|. ..-..++||-|+-.+
T Consensus 7 Veiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 7 VEIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLII 54 (67)
T ss_pred EEeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEE
Confidence 3456666 344456789999 9984 4444443 345678999999875
No 7
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=94.68 E-value=0.025 Score=39.38 Aligned_cols=28 Identities=25% Similarity=0.714 Sum_probs=19.6
Q ss_pred CCcceecCcccccc--hhhHHHHhhhhccc
Q 030491 72 ESKVTVCPICSVKV--ARDMLSHITLQHGH 99 (176)
Q Consensus 72 e~k~vVCPICaa~~--s~d~l~HL~~rH~~ 99 (176)
......||||.+.+ ++|+-+||-+.|+.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 34568999999986 78999999999975
No 8
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=93.72 E-value=0.057 Score=31.50 Aligned_cols=21 Identities=33% Similarity=0.668 Sum_probs=18.9
Q ss_pred cccCCCCCCCCCHHHHHhhhh
Q 030491 46 DFPCPYCYEDFDIASLCSHLE 66 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~ 66 (176)
..+||+||..|....|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 568999999999999999964
No 9
>PLN03086 PRLI-interacting factor K; Provisional
Probab=93.43 E-value=0.089 Score=50.86 Aligned_cols=49 Identities=22% Similarity=0.482 Sum_probs=38.8
Q ss_pred CCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc-chhhHHHHhhhhc
Q 030491 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK-VARDMLSHITLQH 97 (176)
Q Consensus 44 r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~-~s~d~l~HL~~rH 97 (176)
..-+.||+|++.|....|-.|....| +.+.|| |... ...+|..|+....
T Consensus 451 ~~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~thC 500 (567)
T PLN03086 451 KNHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQASTC 500 (567)
T ss_pred ccCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhccC
Confidence 34679999999899999999999866 679999 9654 4678888876433
No 10
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=93.10 E-value=0.051 Score=29.82 Aligned_cols=21 Identities=24% Similarity=0.550 Sum_probs=15.4
Q ss_pred ccCCCCCC-CCCHHHHHhhhhh
Q 030491 47 FPCPYCYE-DFDIASLCSHLED 67 (176)
Q Consensus 47 F~CPFC~e-~fDv~~L~~H~~e 67 (176)
|.||.|++ --+...|..|+..
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 67888888 5566777777765
No 11
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.41 E-value=0.09 Score=36.71 Aligned_cols=49 Identities=20% Similarity=0.517 Sum_probs=15.5
Q ss_pred cCCCCCC-CCCHHHHHhhhhhhccCCCc---------------------ceecCcccccc--hhhHHHHhhhh
Q 030491 48 PCPYCYE-DFDIASLCSHLEDEHSCESK---------------------VTVCPICSVKV--ARDMLSHITLQ 96 (176)
Q Consensus 48 ~CPFC~e-~fDv~~L~~H~~eeH~~e~k---------------------~vVCPICaa~~--s~d~l~HL~~r 96 (176)
.|+||+. --++..|..|+...|.+... ...|++|.... ...+..||...
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 45688999999999986321 13499998875 56889999754
No 12
>PHA00732 hypothetical protein
Probab=91.34 E-value=0.24 Score=36.17 Aligned_cols=42 Identities=29% Similarity=0.652 Sum_probs=32.0
Q ss_pred ccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccchhhHHHHh
Q 030491 47 FPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (176)
Q Consensus 47 F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~d~l~HL 93 (176)
|.|+.|++ --....|..|....|.. ..|++|...-. ++..|+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~-~l~~H~ 44 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR-RLNQHF 44 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC-Chhhhh
Confidence 78999999 44788899999866653 26999987654 466666
No 13
>PHA00733 hypothetical protein
Probab=90.96 E-value=0.37 Score=37.82 Aligned_cols=50 Identities=26% Similarity=0.618 Sum_probs=37.5
Q ss_pred CcccCCCCCCC-CCHHHHHhhhhhhccCCCcceecCcccccc--hhhHHHHhhhhcc
Q 030491 45 PDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQHG 98 (176)
Q Consensus 45 ~~F~CPFC~e~-fDv~~L~~H~~eeH~~e~k~vVCPICaa~~--s~d~l~HL~~rH~ 98 (176)
..|.|+.|++. -....|..|... | .....|++|.... ..+|..|+..-|+
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 36999999994 556778888874 2 2346999997764 6788999887775
No 14
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.63 E-value=0.24 Score=39.27 Aligned_cols=38 Identities=18% Similarity=0.535 Sum_probs=26.2
Q ss_pred CCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 43 ~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
....|.||.|+..|+..+-..... . ....+||.|-..+
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEE
Confidence 466999999999666544333222 1 3458999998875
No 15
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=90.58 E-value=0.2 Score=27.95 Aligned_cols=24 Identities=29% Similarity=0.635 Sum_probs=16.2
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhcc
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHS 70 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~ 70 (176)
|.||+|.-.-....|..|++..|+
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 678888772237788888888774
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=88.78 E-value=0.48 Score=45.96 Aligned_cols=37 Identities=19% Similarity=0.493 Sum_probs=23.7
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
.+.|| |+..+....|..|... |+. .+.+.|+.|...+
T Consensus 478 pv~Cp-Cg~~~~R~~L~~H~~t-hCp-~Kpi~C~fC~~~v 514 (567)
T PLN03086 478 PLQCP-CGVVLEKEQMVQHQAS-TCP-LRLITCRFCGDMV 514 (567)
T ss_pred CccCC-CCCCcchhHHHhhhhc-cCC-CCceeCCCCCCcc
Confidence 46777 7776677777777643 443 3667777776554
No 17
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=88.78 E-value=0.32 Score=43.49 Aligned_cols=37 Identities=24% Similarity=0.600 Sum_probs=25.8
Q ss_pred CCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 44 r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
+..|.||+|++ .+....|--|+... .-.-+|+||-..
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH----~l~c~C~iCGKa 196 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTH----TLPCECGICGKA 196 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhcc----CCCccccccccc
Confidence 56788888888 88888888888754 124455555544
No 18
>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=88.63 E-value=0.18 Score=32.35 Aligned_cols=33 Identities=30% Similarity=0.649 Sum_probs=20.8
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccchhhH
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDM 89 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~d~ 89 (176)
|.||.|+... + ..+ ......||+.|-..+..+.
T Consensus 1 m~Cp~Cg~~~-~------~~D---~~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VFD---PERGELVCPNCGLVLEENI 33 (43)
T ss_dssp ESBTTTSSSE-E------EEE---TTTTEEEETTT-BBEE-TT
T ss_pred CCCcCCcCCc-e------EEc---CCCCeEECCCCCCEeeccc
Confidence 6899999832 1 111 4466789999988775544
No 19
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=88.61 E-value=0.11 Score=34.90 Aligned_cols=31 Identities=26% Similarity=0.590 Sum_probs=19.8
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccCCC---cceecCcccc
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSCES---KVTVCPICSV 83 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~e~---k~vVCPICaa 83 (176)
.-+|||||. .+.+.. ....+. -.|.|..|.+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 568999997 554433 222222 4678999977
No 20
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=88.15 E-value=0.19 Score=36.11 Aligned_cols=30 Identities=20% Similarity=0.473 Sum_probs=21.4
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.=+|||||. .+.+. |....-.++|.-|-+.
T Consensus 6 lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVK---------AISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEE---------ecCceEEEEcCCCCcC
Confidence 458999999 66554 2333446999999886
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=87.56 E-value=0.18 Score=34.76 Aligned_cols=30 Identities=20% Similarity=0.678 Sum_probs=21.7
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.|.||-||+.+++.... ..-.|.||.|.+.
T Consensus 2 ~~~CP~CG~~iev~~~~---------~GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPE---------LGELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCc---------cCCEEeCCCCCCE
Confidence 58999999977554332 1337899999876
No 22
>PHA02768 hypothetical protein; Provisional
Probab=87.55 E-value=0.5 Score=32.86 Aligned_cols=35 Identities=23% Similarity=0.444 Sum_probs=26.3
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.|.||.||+ =...+.|..|....+ ++..|..|..-
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~----k~~kc~~C~k~ 40 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN----TNLKLSNCKRI 40 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC----CcccCCcccce
Confidence 489999999 556778999999844 45567777553
No 23
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=86.98 E-value=0.28 Score=41.74 Aligned_cols=44 Identities=25% Similarity=0.709 Sum_probs=27.6
Q ss_pred CCcccCCCCCCCCC--HHHHHhh-----hhhhcc--------------CCCcceecCcccccchh
Q 030491 44 RPDFPCPYCYEDFD--IASLCSH-----LEDEHS--------------CESKVTVCPICSVKVAR 87 (176)
Q Consensus 44 r~~F~CPFC~e~fD--v~~L~~H-----~~eeH~--------------~e~k~vVCPICaa~~s~ 87 (176)
...|.||.|.+.+. +...|.| |....- ...+...||+|...++.
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 45799999988332 3445666 343321 12345689999998754
No 24
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=86.59 E-value=0.53 Score=29.01 Aligned_cols=33 Identities=18% Similarity=0.501 Sum_probs=19.8
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.+.||.|+..|.+..- ....+...+.||.|-..
T Consensus 2 ~~~CP~C~~~~~v~~~------~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDS------QLGANGGKVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCEEEeCHH------HcCCCCCEEECCCCCCE
Confidence 3689999984443321 11233347889999754
No 25
>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=86.34 E-value=0.15 Score=31.49 Aligned_cols=32 Identities=19% Similarity=0.616 Sum_probs=21.8
Q ss_pred CcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.+|.||-||..|++..-. .+...++||.|.+.
T Consensus 4 Y~y~C~~Cg~~fe~~~~~--------~~~~~~~CP~Cg~~ 35 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKI--------SDDPLATCPECGGD 35 (41)
T ss_pred EEEEcCCCCCEEEEEEec--------CCCCCCCCCCCCCc
Confidence 368999999976643211 22567889999874
No 26
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=86.33 E-value=0.58 Score=41.91 Aligned_cols=47 Identities=21% Similarity=0.467 Sum_probs=24.1
Q ss_pred cccCCCCCCCCCHHHHH-hhhhhhccCCCcceecCcccccc--hhhHHHHhh
Q 030491 46 DFPCPYCYEDFDIASLC-SHLEDEHSCESKVTVCPICSVKV--ARDMLSHIT 94 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~-~H~~eeH~~e~k~vVCPICaa~~--s~d~l~HL~ 94 (176)
-+.|++||+-|+..=|. -|+... ..-|+-.||.|..-. -.|+-.||.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTH--TGEKPF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTH--TGEKPFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred CcccccccccccchHHhhcccccc--cCCCCccCCcccchhcchHHHHHHHH
Confidence 35566666666654333 344432 334555666665443 346666654
No 27
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=84.82 E-value=0.37 Score=36.94 Aligned_cols=33 Identities=18% Similarity=0.520 Sum_probs=20.9
Q ss_pred CCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 44 r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
...|.||||++ -+.+ .-.+ ..--++||+|-..-
T Consensus 19 pt~f~CP~Cge~~v~v-------~~~k--~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISV-------KIKK--NIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeee-------ecCC--CcceEECCCCCCcc
Confidence 45899999996 2221 1111 24458999997754
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=83.82 E-value=0.66 Score=32.28 Aligned_cols=26 Identities=35% Similarity=0.884 Sum_probs=21.1
Q ss_pred CcccCCCCCCCC-CHHHHHhhhhhhcc
Q 030491 45 PDFPCPYCYEDF-DIASLCSHLEDEHS 70 (176)
Q Consensus 45 ~~F~CPFC~e~f-Dv~~L~~H~~eeH~ 70 (176)
..|.|++|++.| +..+|..|+...+-
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 89999999998643
No 29
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=83.18 E-value=0.3 Score=41.14 Aligned_cols=17 Identities=24% Similarity=0.729 Sum_probs=13.5
Q ss_pred cccCCCCCCCCCHHHHH
Q 030491 46 DFPCPYCYEDFDIASLC 62 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~ 62 (176)
+++||+|+..|....+.
T Consensus 5 ~~~CPvC~~~F~~~~vr 21 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVR 21 (214)
T ss_pred ceECCCCCCeeeeeEEE
Confidence 68999999988876443
No 30
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=81.76 E-value=1.3 Score=26.06 Aligned_cols=20 Identities=30% Similarity=0.796 Sum_probs=11.9
Q ss_pred ccCCCCCCCCCHHHHHhhhh
Q 030491 47 FPCPYCYEDFDIASLCSHLE 66 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~ 66 (176)
..||.|++.+....+-.|++
T Consensus 2 v~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVPENLINSHLD 21 (26)
T ss_pred CcCCCCcCcccHHHHHHHHH
Confidence 35666666656666666655
No 31
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=80.26 E-value=1 Score=42.97 Aligned_cols=33 Identities=33% Similarity=0.712 Sum_probs=28.4
Q ss_pred CCCCcccCCCCCCCC-CHHHHHhhhhhhccCCCc
Q 030491 42 DVRPDFPCPYCYEDF-DIASLCSHLEDEHSCESK 74 (176)
Q Consensus 42 d~r~~F~CPFC~e~f-Dv~~L~~H~~eeH~~e~k 74 (176)
+.+.-|.||+|.++| +...|-+|++.+|..|-.
T Consensus 11 ~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ed~ 44 (505)
T KOG1842|consen 11 EILEGFLCPICLLDLPNLSALNDHLDVEHFEEDE 44 (505)
T ss_pred hhhhcccCchHhhhhhhHHHHHHHHhhhccccch
Confidence 567789999999966 478899999999999774
No 32
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=80.03 E-value=0.74 Score=30.02 Aligned_cols=31 Identities=19% Similarity=0.712 Sum_probs=21.5
Q ss_pred CcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccc
Q 030491 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa 83 (176)
.+|.|+-||..|++. .... +...+.||.|..
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 379999999988743 1111 245678999987
No 33
>PHA00616 hypothetical protein
Probab=79.72 E-value=1.1 Score=29.82 Aligned_cols=26 Identities=19% Similarity=0.268 Sum_probs=20.9
Q ss_pred ccCCCCCC-CCCHHHHHhhhhhhccCC
Q 030491 47 FPCPYCYE-DFDIASLCSHLEDEHSCE 72 (176)
Q Consensus 47 F~CPFC~e-~fDv~~L~~H~~eeH~~e 72 (176)
|.||.||. =....+|..|+...|.-+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~ 28 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQN 28 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCC
Confidence 78999998 667788889998887753
No 34
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=79.72 E-value=0.62 Score=30.73 Aligned_cols=45 Identities=38% Similarity=0.806 Sum_probs=29.5
Q ss_pred cccCCC--CCCCCCHHHHHhhhhhhccCCCcceecCc----ccccc-hhhHHHH
Q 030491 46 DFPCPY--CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVKV-ARDMLSH 92 (176)
Q Consensus 46 ~F~CPF--C~e~fDv~~L~~H~~eeH~~e~k~vVCPI----Caa~~-s~d~l~H 92 (176)
...||+ |.+.+-...|-.|+..+ =.-+.+.||. |..++ ..++..|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~--C~~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENE--CPKRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTT--STTSEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHcc--CCCCcEECCCCCCCCCCccchhHHhCC
Confidence 568999 65678888999999865 3346889999 98876 4456554
No 35
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=79.57 E-value=0.75 Score=46.51 Aligned_cols=51 Identities=24% Similarity=0.481 Sum_probs=40.4
Q ss_pred CCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccc--hhhHHHHhh
Q 030491 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHIT 94 (176)
Q Consensus 44 r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~--s~d~l~HL~ 94 (176)
-+..+||||.. .-...+|.+|+.-.|---.-+.-|+.|.... -..+-+|+.
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~ 261 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQ 261 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHH
Confidence 35689999999 6678999999999999877788899998874 234555554
No 36
>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=79.32 E-value=2.1 Score=28.08 Aligned_cols=27 Identities=7% Similarity=0.113 Sum_probs=18.9
Q ss_pred CCCCCHHHHHhhhhhhccCCCcceecCcccccch
Q 030491 53 YEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (176)
Q Consensus 53 ~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s 86 (176)
|.-|+...+..++.. ...||+|....+
T Consensus 20 G~v~~~~~i~~~~~~-------~~~cP~~~~~~~ 46 (63)
T smart00504 20 GQTYERRAIEKWLLS-------HGTDPVTGQPLT 46 (63)
T ss_pred CCEEeHHHHHHHHHH-------CCCCCCCcCCCC
Confidence 445777777777765 358999977653
No 37
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=78.88 E-value=0.57 Score=32.08 Aligned_cols=12 Identities=50% Similarity=1.270 Sum_probs=9.1
Q ss_pred ccCCCCCCCCCH
Q 030491 47 FPCPYCYEDFDI 58 (176)
Q Consensus 47 F~CPFC~e~fDv 58 (176)
+.|||||+.+++
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 469999996553
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=78.06 E-value=2.9 Score=22.01 Aligned_cols=22 Identities=27% Similarity=0.585 Sum_probs=15.4
Q ss_pred ccCCCCCC-CCCHHHHHhhhhhhc
Q 030491 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (176)
Q Consensus 47 F~CPFC~e-~fDv~~L~~H~~eeH 69 (176)
|.|+.|++ --....|..|.. .|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-TH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hh
Confidence 56888888 455667777776 44
No 39
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.18 E-value=2 Score=30.46 Aligned_cols=32 Identities=31% Similarity=0.689 Sum_probs=24.0
Q ss_pred CCcccCCCCCCC-CCHHHHHhhhhhhccCCCcceecCccc
Q 030491 44 RPDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICS 82 (176)
Q Consensus 44 r~~F~CPFC~e~-fDv~~L~~H~~eeH~~e~k~vVCPICa 82 (176)
-..|.||-||+. +-. |..|... +...+||-|-
T Consensus 23 ~~~F~CPnCG~~~I~R---C~~CRk~----~~~Y~CP~CG 55 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR---CEKCRKQ----SNPYTCPKCG 55 (59)
T ss_pred cCEeeCCCCCCeeEee---chhHHhc----CCceECCCCC
Confidence 468999999994 544 5666554 6788999985
No 40
>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=77.17 E-value=1.4 Score=24.85 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=17.3
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhc
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEH 69 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH 69 (176)
.|.|..|++ =-+...|..|....|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 377888888 556778888875544
No 41
>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=76.69 E-value=0.82 Score=28.16 Aligned_cols=24 Identities=29% Similarity=0.899 Sum_probs=12.4
Q ss_pred cCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccc
Q 030491 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (176)
Q Consensus 48 ~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa 83 (176)
.||.|+.++.. .+....|||-|..
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 58888774443 5677889999864
No 42
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=76.57 E-value=1.1 Score=32.92 Aligned_cols=34 Identities=21% Similarity=0.615 Sum_probs=14.4
Q ss_pred CCcccCCCCC-C-CCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 44 RPDFPCPYCY-E-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 44 r~~F~CPFC~-e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
...|.||||+ + .+.+ .-.-....-.+.|-+|-..
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 3589999998 4 3322 1122233446889999654
No 43
>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=76.48 E-value=1.8 Score=28.85 Aligned_cols=9 Identities=22% Similarity=0.490 Sum_probs=4.2
Q ss_pred CCHHHHHhh
Q 030491 56 FDIASLCSH 64 (176)
Q Consensus 56 fDv~~L~~H 64 (176)
+...+|..|
T Consensus 12 Y~~~~LlqH 20 (43)
T PF03470_consen 12 YKYRELLQH 20 (43)
T ss_pred eehhHHHHH
Confidence 444444444
No 44
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=76.45 E-value=1.1 Score=33.05 Aligned_cols=27 Identities=30% Similarity=0.869 Sum_probs=18.4
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccc
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa 83 (176)
.|+||-||. -|+.. .+...-+||||-=
T Consensus 1 K~~CPCCg~~Tl~~~-----------~~~~ydIC~VC~W 28 (78)
T PF14206_consen 1 KYPCPCCGYYTLEER-----------GEGTYDICPVCFW 28 (78)
T ss_pred CccCCCCCcEEeccC-----------CCcCceECCCCCc
Confidence 379999988 65532 2233679999954
No 45
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=76.41 E-value=1.5 Score=28.35 Aligned_cols=28 Identities=18% Similarity=0.687 Sum_probs=16.6
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
+|.||-||..|+... ......||.|...
T Consensus 3 ~y~C~~CG~~~~~~~-----------~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDE-----------YGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECC-----------CCCceECCCCCCe
Confidence 577777777555411 1115778877664
No 46
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=75.62 E-value=0.83 Score=34.70 Aligned_cols=34 Identities=21% Similarity=0.466 Sum_probs=21.7
Q ss_pred CCCCCCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 40 EDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 40 ddd~r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
|..+.+.|.||||+. .+... ...--.|--|-..+
T Consensus 30 e~~q~a~y~CpfCgk~~vkR~------------a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 30 EISQHAKYFCPFCGKHAVKRQ------------AVGIWRCKGCKKTV 64 (90)
T ss_pred HHHHhCCccCCCCCCCceeee------------eeEEEEcCCCCCEE
Confidence 335688999999987 55332 12334577776664
No 47
>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=75.58 E-value=0.98 Score=27.64 Aligned_cols=24 Identities=33% Similarity=0.829 Sum_probs=14.0
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccc
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa 83 (176)
|.|+.||.-++... ..-+||+|.+
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCC
Confidence 56777776333221 4557888865
No 48
>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=75.50 E-value=2.4 Score=28.08 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=20.3
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhcc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHS 70 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~ 70 (176)
.+.||.|...+.. .|..|+...|+
T Consensus 31 ~v~CPiC~~~~~~-~l~~Hl~~~H~ 54 (54)
T PF05605_consen 31 NVVCPICSSRVTD-NLIRHLNSQHR 54 (54)
T ss_pred CccCCCchhhhhh-HHHHHHHHhcC
Confidence 6999999986653 99999998884
No 49
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=75.48 E-value=1.7 Score=40.15 Aligned_cols=58 Identities=29% Similarity=0.559 Sum_probs=36.4
Q ss_pred cccCCCCCCCCCHHHH---HhhhhhhccCCCc-ceecCcccccc--------------------------hhhHHHHhhh
Q 030491 46 DFPCPYCYEDFDIASL---CSHLEDEHSCESK-VTVCPICSVKV--------------------------ARDMLSHITL 95 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L---~~H~~eeH~~e~k-~vVCPICaa~~--------------------------s~d~l~HL~~ 95 (176)
.-.|--|+.-+-+-+= |+|+-=.-+.-.. -.+||.|..+| -+||..||++
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 4556666654444332 4444333332111 46899999885 3699999999
Q ss_pred hccchhhh
Q 030491 96 QHGHLFKL 103 (176)
Q Consensus 96 rH~~~~k~ 103 (176)
+|+...+-
T Consensus 170 rH~~~~~p 177 (389)
T KOG2932|consen 170 RHGSLLQP 177 (389)
T ss_pred hhccccCC
Confidence 99976644
No 50
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.76 E-value=1.2 Score=39.54 Aligned_cols=12 Identities=33% Similarity=0.982 Sum_probs=9.0
Q ss_pred CcccCCCCCCCC
Q 030491 45 PDFPCPYCYEDF 56 (176)
Q Consensus 45 ~~F~CPFC~e~f 56 (176)
.++.||+|+--|
T Consensus 18 k~ieCPvC~tkF 29 (267)
T COG1655 18 KTIECPVCNTKF 29 (267)
T ss_pred ceeccCcccchh
Confidence 379999996544
No 51
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=74.60 E-value=2 Score=40.70 Aligned_cols=98 Identities=18% Similarity=0.269 Sum_probs=54.4
Q ss_pred CCCCCCCCCCCCcccCCCCCC---CCCHHHHHhhhhhhccCCCcceecCcccccc-----------hhhHHHHhhhhccc
Q 030491 34 IDDFEVEDDVRPDFPCPYCYE---DFDIASLCSHLEDEHSCESKVTVCPICSVKV-----------ARDMLSHITLQHGH 99 (176)
Q Consensus 34 ~d~~~~ddd~r~~F~CPFC~e---~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~-----------s~d~l~HL~~rH~~ 99 (176)
+++.+.++..++.|.||+|.. .||...|.. ++...-.|-.|-.-+ +...+++++-|=..
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 444445556789999999988 455555554 334566788876542 34556677666666
Q ss_pred hhhhhhcccccc---------cCCCCchhHhhhhhhhhhhhhHHHhcc
Q 030491 100 LFKLQRRRRLRR---------VAIPSSQALSLLGRDLREAHLQVLLGE 138 (176)
Q Consensus 100 ~~k~~r~rr~rr---------~~~p~~s~ls~l~kelre~~lq~llg~ 138 (176)
.++.-++--.-+ -..|..+-=+++-..++-+.+-++-|+
T Consensus 189 i~d~Lk~~e~i~~l~~~~n~~~~~~~p~~~~~~~~~~~~a~~a~~~G~ 236 (436)
T KOG2593|consen 189 IIDLLKELEGIKPLAPPQNEPKDTPIPALESFLALQADTAKAASENGG 236 (436)
T ss_pred HHHHHHHhhccccccccccCCccCcCccccccccccccchhhhhhccC
Confidence 665421111100 011121233455556666666666664
No 52
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=74.56 E-value=2.9 Score=39.34 Aligned_cols=55 Identities=25% Similarity=0.431 Sum_probs=42.8
Q ss_pred CCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCccccc--------------------------------------
Q 030491 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK-------------------------------------- 84 (176)
Q Consensus 44 r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~-------------------------------------- 84 (176)
.--=.|-||.. =+|..+|..||...|- .|-||..+
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 34557999999 8899999999999985 45555443
Q ss_pred c-hhhHHHHhhhhccchhhhh
Q 030491 85 V-ARDMLSHITLQHGHLFKLQ 104 (176)
Q Consensus 85 ~-s~d~l~HL~~rH~~~~k~~ 104 (176)
+ -..++.||+..||...+.+
T Consensus 292 ~~~~el~~h~~~~h~~~~~~~ 312 (493)
T COG5236 292 PYHTELLEHLTRFHKVNARLS 312 (493)
T ss_pred ccHHHHHHHHHHHhhcccccC
Confidence 1 2478999999999988764
No 53
>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=73.46 E-value=2.2 Score=34.80 Aligned_cols=54 Identities=28% Similarity=0.645 Sum_probs=32.6
Q ss_pred CcccCCC----CCCCCCHHHHHhhhhhhccCCCcceecCc----cccc-chhhHHHHhhhhccchh
Q 030491 45 PDFPCPY----CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVK-VARDMLSHITLQHGHLF 101 (176)
Q Consensus 45 ~~F~CPF----C~e~fDv~~L~~H~~eeH~~e~k~vVCPI----Caa~-~s~d~l~HL~~rH~~~~ 101 (176)
-.|+|+| |.+.+-......|.+. -.-++..||+ |.-. ...++..|+...|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~~---C~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEEE---CPFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHHT----TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhcc---CCCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 3799999 9888887777777643 2346788999 7543 46799999999998743
No 54
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=71.05 E-value=1.8 Score=28.86 Aligned_cols=30 Identities=27% Similarity=0.652 Sum_probs=16.4
Q ss_pred cCCCCCC-CCCHHHHHhhhhhhcc-C-CCcceecCccccc
Q 030491 48 PCPYCYE-DFDIASLCSHLEDEHS-C-ESKVTVCPICSVK 84 (176)
Q Consensus 48 ~CPFC~e-~fDv~~L~~H~~eeH~-~-e~k~vVCPICaa~ 84 (176)
+|||||- +.-+. ..+. . ......|+-|-+.
T Consensus 3 PCPfCGg~~~~~~-------~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 3 PCPFCGGADVYLR-------RGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCcceeeE-------eccCCCCCEEEEECCCCCCC
Confidence 7999987 43221 1111 1 2223469999765
No 55
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=70.31 E-value=1.5 Score=27.19 Aligned_cols=26 Identities=27% Similarity=0.599 Sum_probs=16.5
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.|.|+.||.-++.. ...-+||||-+.
T Consensus 2 ~~~C~~CG~i~~g~-------------~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGE-------------EAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECC-------------cCCCcCcCCCCc
Confidence 47888898733321 123599999774
No 56
>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=70.16 E-value=1.2 Score=33.91 Aligned_cols=17 Identities=24% Similarity=0.765 Sum_probs=13.1
Q ss_pred CCCCCCcccCCCCCC-CC
Q 030491 40 EDDVRPDFPCPYCYE-DF 56 (176)
Q Consensus 40 ddd~r~~F~CPFC~e-~f 56 (176)
|..+...|.||||+. .+
T Consensus 29 e~~q~a~y~CpfCgk~~v 46 (91)
T TIGR00280 29 EIQQKAKYVCPFCGKKTV 46 (91)
T ss_pred HHHHhcCccCCCCCCCce
Confidence 335688999999987 44
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=69.31 E-value=5.7 Score=32.05 Aligned_cols=33 Identities=21% Similarity=0.388 Sum_probs=24.8
Q ss_pred CCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 43 ~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
....|.||-|+.-++..+-.+ ..-.||+|-...
T Consensus 106 ~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAML 138 (158)
T ss_pred CCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEe
Confidence 456899999999666555554 267999998875
No 58
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=68.96 E-value=3.7 Score=33.94 Aligned_cols=33 Identities=24% Similarity=0.429 Sum_probs=23.8
Q ss_pred CCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 43 ~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
....|.||-|+.-|+..+-.+ ..-.||+|-...
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 367999998875
No 59
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=68.43 E-value=1.4 Score=33.42 Aligned_cols=17 Identities=29% Similarity=0.755 Sum_probs=13.0
Q ss_pred CCCCCCcccCCCCCC-CC
Q 030491 40 EDDVRPDFPCPYCYE-DF 56 (176)
Q Consensus 40 ddd~r~~F~CPFC~e-~f 56 (176)
|..+.+.|+||||+. .+
T Consensus 30 e~~q~a~y~CpfCgk~~v 47 (90)
T PRK03976 30 EEKMRAKHVCPVCGRPKV 47 (90)
T ss_pred HHHHhcCccCCCCCCCce
Confidence 335678999999987 44
No 60
>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=68.17 E-value=5.3 Score=27.98 Aligned_cols=36 Identities=19% Similarity=0.362 Sum_probs=23.1
Q ss_pred CCcccCCCCCC------------CCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 44 RPDFPCPYCYE------------DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 44 r~~F~CPFC~e------------~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
+..|.||.|++ -||...+..++.. ...+||+|...+
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l 49 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPL 49 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcC
Confidence 35788888854 4677777777766 567999996665
No 61
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=67.72 E-value=3.1 Score=24.59 Aligned_cols=11 Identities=45% Similarity=0.993 Sum_probs=9.3
Q ss_pred CCcccCCCCCC
Q 030491 44 RPDFPCPYCYE 54 (176)
Q Consensus 44 r~~F~CPFC~e 54 (176)
-..|.||-||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45899999986
No 62
>PF12773 DZR: Double zinc ribbon
Probab=67.09 E-value=3 Score=26.86 Aligned_cols=28 Identities=21% Similarity=0.562 Sum_probs=19.3
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccch
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s 86 (176)
=.||.||..+. ..+...++||.|.+.+.
T Consensus 13 ~fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 13 KFCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred cCChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 35777877665 44556788999987653
No 63
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=66.62 E-value=5.1 Score=38.24 Aligned_cols=41 Identities=32% Similarity=0.368 Sum_probs=32.3
Q ss_pred CCcccCCCCCC-CCCHHHHHhhhhhhccCCCcc---eecCccccc
Q 030491 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKV---TVCPICSVK 84 (176)
Q Consensus 44 r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~---vVCPICaa~ 84 (176)
+.--.||+|.+ -.|..++..|+..+|..+-.+ -+.|-+...
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~ 99 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDD 99 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCH
Confidence 44578999999 999999999999999986543 455665544
No 64
>PRK12495 hypothetical protein; Provisional
Probab=66.42 E-value=3.8 Score=35.82 Aligned_cols=29 Identities=21% Similarity=0.478 Sum_probs=22.5
Q ss_pred CcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccch
Q 030491 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s 86 (176)
..|.||.||..+- .. ...++||+|-..+.
T Consensus 41 sa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIF------------RH-DGQEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCccc------------CC-CCeeECCCCCCccc
Confidence 4699999999554 22 56789999998874
No 65
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=65.61 E-value=2.9 Score=32.68 Aligned_cols=36 Identities=19% Similarity=0.452 Sum_probs=21.5
Q ss_pred CCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 44 r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
..+|+||||+...-++-+ -.-...--.++|-+|-..
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 458999999983222211 111223346889999654
No 66
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=64.81 E-value=6 Score=28.29 Aligned_cols=34 Identities=29% Similarity=0.747 Sum_probs=22.0
Q ss_pred CCCCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCccc
Q 030491 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICS 82 (176)
Q Consensus 42 d~r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICa 82 (176)
|.-..|+||-||| .+-.-.-| .. -.+..+||-|-
T Consensus 23 e~~v~F~CPnCGe~~I~Rc~~C---Rk----~g~~Y~Cp~CG 57 (61)
T COG2888 23 ETAVKFPCPNCGEVEIYRCAKC---RK----LGNPYRCPKCG 57 (61)
T ss_pred CceeEeeCCCCCceeeehhhhH---HH----cCCceECCCcC
Confidence 3456899999997 55443332 22 25677899884
No 67
>PF13395 HNH_4: HNH endonuclease
Probab=64.57 E-value=3.7 Score=27.37 Aligned_cols=14 Identities=43% Similarity=1.058 Sum_probs=12.3
Q ss_pred CCCCCCCCCHHHHH
Q 030491 49 CPYCYEDFDIASLC 62 (176)
Q Consensus 49 CPFC~e~fDv~~L~ 62 (176)
|||||+.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999988864
No 68
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=63.53 E-value=5 Score=34.18 Aligned_cols=43 Identities=21% Similarity=0.589 Sum_probs=26.7
Q ss_pred CcccCCCCCCCCCHHH----HHhhhhhhccC---CCcceecCcccccchh
Q 030491 45 PDFPCPYCYEDFDIAS----LCSHLEDEHSC---ESKVTVCPICSVKVAR 87 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~----L~~H~~eeH~~---e~k~vVCPICaa~~s~ 87 (176)
..|.||.|-+.+.... =|-|+-=.-+. =.+.++||+|-.+++.
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 4699999977555444 23343322222 2346899999988754
No 69
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=63.12 E-value=4.3 Score=26.71 Aligned_cols=28 Identities=21% Similarity=0.553 Sum_probs=21.3
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
.|.|.-||.+|++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58899999877754 34578999998765
No 70
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=62.72 E-value=6.3 Score=27.00 Aligned_cols=33 Identities=15% Similarity=0.438 Sum_probs=17.3
Q ss_pred CCCcccCCCCCC-------------CCCHHHHHhhhhhhccCCCcceecCc
Q 030491 43 VRPDFPCPYCYE-------------DFDIASLCSHLEDEHSCESKVTVCPI 80 (176)
Q Consensus 43 ~r~~F~CPFC~e-------------~fDv~~L~~H~~eeH~~e~k~vVCPI 80 (176)
....|.||.... -|+...+..++ ...+.+.||+
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 344677776643 45666666666 3456788888
No 71
>PF15616 TerY-C: TerY-C metal binding domain
Probab=62.56 E-value=2.1 Score=34.44 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=28.4
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccC-CCcceecCcccccchh
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSC-ESKVTVCPICSVKVAR 87 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~-e~k~vVCPICaa~~s~ 87 (176)
=.||+||..+-.+-. =|-.-|+. +...++||-|-....-
T Consensus 78 PgCP~CGn~~~fa~C--~CGkl~Ci~g~~~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC--GCGKLFCIDGEGEVTCPWCGNEGSF 117 (131)
T ss_pred CCCCCCcChhcEEEe--cCCCEEEeCCCCCEECCCCCCeeee
Confidence 579999985444322 48888884 5668999999887543
No 72
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=62.40 E-value=4.8 Score=33.49 Aligned_cols=25 Identities=36% Similarity=0.822 Sum_probs=18.4
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.+.||.||-- |.. -.+.+||||-+.
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 8999999741 222 457899999864
No 73
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=62.10 E-value=7.7 Score=32.09 Aligned_cols=46 Identities=20% Similarity=0.346 Sum_probs=31.3
Q ss_pred CCCCCCCCCCCCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccchhhHHHHhh
Q 030491 33 SIDDFEVEDDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHIT 94 (176)
Q Consensus 33 g~d~~~~ddd~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~d~l~HL~ 94 (176)
|+..+..+++..+.=.||.||. ...+...||.|....-+|..+=++
T Consensus 296 ~~~~v~~~~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~N 341 (364)
T COG0675 296 GGIVVKVVPPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALN 341 (364)
T ss_pred CCeEEEECCCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHHH
Confidence 4444444444556678999998 336788999999887666554333
No 74
>PRK00420 hypothetical protein; Validated
Probab=60.83 E-value=6.1 Score=30.97 Aligned_cols=27 Identities=22% Similarity=0.369 Sum_probs=19.1
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
-.||.||-.|-. .....++||+|...+
T Consensus 24 ~~CP~Cg~pLf~------------lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFE------------LKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCccee------------cCCCceECCCCCCee
Confidence 589999974311 134579999998864
No 75
>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=58.50 E-value=2.5 Score=27.07 Aligned_cols=31 Identities=23% Similarity=0.635 Sum_probs=21.0
Q ss_pred CcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccc
Q 030491 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa 83 (176)
-+|.|+=||..|++..- ..+...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~--------~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQS--------ISEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEE--------cCCCCCCcCCCCCC
Confidence 36889999876654321 12356789999976
No 76
>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=58.11 E-value=11 Score=25.57 Aligned_cols=47 Identities=26% Similarity=0.553 Sum_probs=32.3
Q ss_pred cCCCCCCCCCCCCCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccchhhHHH
Q 030491 32 LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLS 91 (176)
Q Consensus 32 ~g~d~~~~ddd~r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~d~l~ 91 (176)
.|+.-+++++ .-.+=.||.||. .-+ ....+..+||.|-....+|+.+
T Consensus 15 ~G~~v~~v~~-~~TSq~C~~CG~~~~~------------~~~~r~~~C~~Cg~~~~rD~na 62 (69)
T PF07282_consen 15 YGIQVVEVDE-AYTSQTCPRCGHRNKK------------RRSGRVFTCPNCGFEMDRDVNA 62 (69)
T ss_pred hCCEEEEECC-CCCccCccCccccccc------------ccccceEEcCCCCCEECcHHHH
Confidence 3555445543 336778999998 333 4566789999999887777654
No 77
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=57.99 E-value=4.6 Score=31.21 Aligned_cols=9 Identities=67% Similarity=1.575 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 030491 46 DFPCPYCYE 54 (176)
Q Consensus 46 ~F~CPFC~e 54 (176)
.++|||||+
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 468999998
No 78
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=56.98 E-value=3 Score=32.03 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=22.3
Q ss_pred CCCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 42 d~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
+.+..+.|+-|+..|..... ...||-|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 34678999999987766533 4679999764
No 79
>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=56.46 E-value=10 Score=21.74 Aligned_cols=23 Identities=35% Similarity=0.686 Sum_probs=17.0
Q ss_pred HHHhhhhhhccCCCcceecCccccc
Q 030491 60 SLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 60 ~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.|..|+.. |..+ ++..||+|...
T Consensus 1 ~l~~H~~~-H~~~-k~~~C~~C~k~ 23 (26)
T PF13465_consen 1 NLRRHMRT-HTGE-KPYKCPYCGKS 23 (26)
T ss_dssp HHHHHHHH-HSSS-SSEEESSSSEE
T ss_pred CHHHHhhh-cCCC-CCCCCCCCcCe
Confidence 47788885 7655 67899999653
No 80
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=56.41 E-value=7.4 Score=36.63 Aligned_cols=35 Identities=31% Similarity=0.747 Sum_probs=20.7
Q ss_pred CCCCCCCCCHHH-----------HHhhhhhhccCCCcceecCccccc
Q 030491 49 CPYCYEDFDIAS-----------LCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 49 CPFC~e~fDv~~-----------L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
||.|-|.+|+.+ .|..|- .|--+.-++.||.|.-+
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 777766555542 333332 12223478999999876
No 81
>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=55.77 E-value=6.9 Score=23.18 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=3.7
Q ss_pred CCCCCCCC
Q 030491 49 CPYCYEDF 56 (176)
Q Consensus 49 CPFC~e~f 56 (176)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 45554433
No 82
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=55.60 E-value=2 Score=35.37 Aligned_cols=40 Identities=25% Similarity=0.613 Sum_probs=19.7
Q ss_pred CCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 44 r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
+-.|.||.|+..+...++.. .+.-.....-..||-|....
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 34799999999666666544 11112234568899998864
No 83
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=55.39 E-value=9.1 Score=24.19 Aligned_cols=20 Identities=30% Similarity=0.753 Sum_probs=12.1
Q ss_pred HHhhhhhhccCCCcceecCccc
Q 030491 61 LCSHLEDEHSCESKVTVCPICS 82 (176)
Q Consensus 61 L~~H~~eeH~~e~k~vVCPICa 82 (176)
+|.-|..... .+.++||+|.
T Consensus 24 ~C~~C~~~~~--~~~~~CP~C~ 43 (44)
T PF14634_consen 24 FCEKCLKKLK--GKSVKCPICR 43 (44)
T ss_pred HHHHHHHhhc--CCCCCCcCCC
Confidence 3444444433 6678888885
No 84
>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=54.37 E-value=5.1 Score=30.44 Aligned_cols=13 Identities=23% Similarity=0.986 Sum_probs=10.2
Q ss_pred CCCCcccCCCCCC
Q 030491 42 DVRPDFPCPYCYE 54 (176)
Q Consensus 42 d~r~~F~CPFC~e 54 (176)
.+...|.||||+.
T Consensus 31 ~q~~ky~Cp~Cgk 43 (90)
T PF01780_consen 31 SQHAKYTCPFCGK 43 (90)
T ss_dssp HHHS-BEESSSSS
T ss_pred HHhCCCcCCCCCC
Confidence 4567899999998
No 85
>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=54.24 E-value=10 Score=29.34 Aligned_cols=33 Identities=24% Similarity=0.666 Sum_probs=23.5
Q ss_pred CCCCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccchh
Q 030491 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (176)
Q Consensus 42 d~r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~ 87 (176)
++-....||-||. =+|+ ...++|||-|.+....
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 4456789999998 4443 2467999999886543
No 86
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=54.21 E-value=8.6 Score=30.10 Aligned_cols=28 Identities=21% Similarity=0.428 Sum_probs=23.0
Q ss_pred ceecCcccccc-----hhhHHHHhhhhccchhh
Q 030491 75 VTVCPICSVKV-----ARDMLSHITLQHGHLFK 102 (176)
Q Consensus 75 ~vVCPICaa~~-----s~d~l~HL~~rH~~~~k 102 (176)
.+.||+|.... ..++..||+.-||-+-+
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 66799999999999763
No 87
>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=54.18 E-value=8.7 Score=32.54 Aligned_cols=36 Identities=31% Similarity=0.572 Sum_probs=23.5
Q ss_pred CCCCCC--CCCHHHHHhhhhhhccC------CCcceecCccccc
Q 030491 49 CPYCYE--DFDIASLCSHLEDEHSC------ESKVTVCPICSVK 84 (176)
Q Consensus 49 CPFC~e--~fDv~~L~~H~~eeH~~------e~k~vVCPICaa~ 84 (176)
||.||. +-...+||.=|-.+... .....+||.|-+.
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 888887 33345777777655442 2345789999764
No 88
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=53.28 E-value=10 Score=26.39 Aligned_cols=25 Identities=32% Similarity=0.861 Sum_probs=17.8
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
-.||.|++.|. .+--.||||.|.+.
T Consensus 6 ~~C~~Cg~~~~-------------~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFK-------------DGDDIVVCPECGAP 30 (54)
T ss_pred ccChhhCCccc-------------CCCCEEECCCCCCc
Confidence 47889988662 12346899999875
No 89
>PRK12496 hypothetical protein; Provisional
Probab=53.07 E-value=9.3 Score=31.12 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=20.0
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccch
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s 86 (176)
.|.||-|++.|+. ....-+||||-..+.
T Consensus 127 ~~~C~gC~~~~~~-------------~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPE-------------DYPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccC-------------CCCCCcCCCCCChhh
Confidence 4889999987753 122358999987653
No 90
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=52.86 E-value=7.1 Score=26.40 Aligned_cols=13 Identities=38% Similarity=0.945 Sum_probs=11.2
Q ss_pred CCCCcccCCCCCC
Q 030491 42 DVRPDFPCPYCYE 54 (176)
Q Consensus 42 d~r~~F~CPFC~e 54 (176)
++..+|.||-|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (50)
T cd00730 30 DLPDDWVCPVCGA 42 (50)
T ss_pred HCCCCCCCCCCCC
Confidence 5678999999987
No 91
>PRK03922 hypothetical protein; Provisional
Probab=52.44 E-value=7 Score=30.94 Aligned_cols=14 Identities=50% Similarity=0.736 Sum_probs=11.4
Q ss_pred cccCCCCCCCCCHH
Q 030491 46 DFPCPYCYEDFDIA 59 (176)
Q Consensus 46 ~F~CPFC~e~fDv~ 59 (176)
.-.||+||++|+-+
T Consensus 49 ~~~cP~cge~~~~a 62 (113)
T PRK03922 49 LTICPKCGEPFDSA 62 (113)
T ss_pred cccCCCCCCcCCcE
Confidence 56899999998743
No 92
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=52.43 E-value=16 Score=22.84 Aligned_cols=30 Identities=27% Similarity=0.745 Sum_probs=19.1
Q ss_pred ccCCCCCCCCCHH--HHHhhhhhhccCCCcceecCccccc
Q 030491 47 FPCPYCYEDFDIA--SLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 47 F~CPFC~e~fDv~--~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
..||-|+..|.+. .| +...+.|.||-|...
T Consensus 3 i~CP~C~~~f~v~~~~l--------~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKL--------PAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHc--------ccCCcEEECCCCCcE
Confidence 5789998844443 32 234567888888653
No 93
>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=52.10 E-value=12 Score=21.89 Aligned_cols=22 Identities=32% Similarity=0.606 Sum_probs=15.7
Q ss_pred cccCCCCCCCCC-HHHHHhhhhh
Q 030491 46 DFPCPYCYEDFD-IASLCSHLED 67 (176)
Q Consensus 46 ~F~CPFC~e~fD-v~~L~~H~~e 67 (176)
.|.|.+|+..|. ...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 477888888555 7777777654
No 94
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=51.93 E-value=7.6 Score=36.21 Aligned_cols=40 Identities=23% Similarity=0.517 Sum_probs=32.2
Q ss_pred cccCCC--CCC-CCCHHHHHhhhhhhccC-----------------CCcceecCcccccc
Q 030491 46 DFPCPY--CYE-DFDIASLCSHLEDEHSC-----------------ESKVTVCPICSVKV 85 (176)
Q Consensus 46 ~F~CPF--C~e-~fDv~~L~~H~~eeH~~-----------------e~k~vVCPICaa~~ 85 (176)
-|.||. |.+ .-++-+|--|...-|+. +.|+.+|+||..+-
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhh
Confidence 489987 878 88899999999888832 44778999998874
No 95
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=51.18 E-value=7.5 Score=30.29 Aligned_cols=14 Identities=50% Similarity=0.904 Sum_probs=11.4
Q ss_pred cccCCCCCCCCCHH
Q 030491 46 DFPCPYCYEDFDIA 59 (176)
Q Consensus 46 ~F~CPFC~e~fDv~ 59 (176)
.-.||+||++|+-.
T Consensus 47 ~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 47 DTICPKCGEELDSA 60 (102)
T ss_pred cccCCCCCCccCce
Confidence 57899999988743
No 96
>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=51.08 E-value=9.4 Score=21.76 Aligned_cols=21 Identities=24% Similarity=0.393 Sum_probs=14.4
Q ss_pred ccCCCCCC-CCCHHHHHhhhhh
Q 030491 47 FPCPYCYE-DFDIASLCSHLED 67 (176)
Q Consensus 47 F~CPFC~e-~fDv~~L~~H~~e 67 (176)
|.|+.|+. =-+...|..|+..
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 67888888 5566677776653
No 97
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=50.74 E-value=7.4 Score=26.61 Aligned_cols=9 Identities=44% Similarity=1.460 Sum_probs=8.2
Q ss_pred cccCCCCCC
Q 030491 46 DFPCPYCYE 54 (176)
Q Consensus 46 ~F~CPFC~e 54 (176)
.|.||+|+.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 899999986
No 98
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=49.28 E-value=3.8 Score=34.67 Aligned_cols=28 Identities=14% Similarity=0.470 Sum_probs=18.1
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCC
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCES 73 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~ 73 (176)
.|.||.|+..+.+.+=-=+|...|.++.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~fd~ 29 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQFDC 29 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCCcc
Confidence 4899999996643322234566777743
No 99
>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=48.69 E-value=10 Score=34.54 Aligned_cols=38 Identities=26% Similarity=0.492 Sum_probs=24.2
Q ss_pred cccCCCCCC--CCCHH----------HHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYE--DFDIA----------SLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e--~fDv~----------~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.+.||.|.. .+.-. .+|..|.+..-. .....||+|-..
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~-~~~~~CP~C~~~ 52 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV-RGSGSCPECDTP 52 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc-CCCCCCCCCCCc
Confidence 368999966 22222 356677777633 345699999654
No 100
>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=47.76 E-value=9.2 Score=25.56 Aligned_cols=13 Identities=38% Similarity=0.945 Sum_probs=8.3
Q ss_pred CCCCcccCCCCCC
Q 030491 42 DVRPDFPCPYCYE 54 (176)
Q Consensus 42 d~r~~F~CPFC~e 54 (176)
++...|.||-|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 30 DLPDDWVCPVCGA 42 (47)
T ss_dssp GS-TT-B-TTTSS
T ss_pred HCCCCCcCcCCCC
Confidence 5677999999986
No 101
>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=47.37 E-value=7.4 Score=25.79 Aligned_cols=14 Identities=29% Similarity=0.591 Sum_probs=7.7
Q ss_pred cCCCCCCCCCHHHH
Q 030491 48 PCPYCYEDFDIASL 61 (176)
Q Consensus 48 ~CPFC~e~fDv~~L 61 (176)
.||.|+.+||...-
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999998887544
No 102
>smart00507 HNHc HNH nucleases.
Probab=47.16 E-value=3.1 Score=25.33 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=13.1
Q ss_pred ccCCCCCCCCCHHHHHhhhhh
Q 030491 47 FPCPYCYEDFDIASLCSHLED 67 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~e 67 (176)
+.|+||+..++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 789999996553223444443
No 103
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.75 E-value=12 Score=21.65 Aligned_cols=8 Identities=38% Similarity=1.003 Sum_probs=5.0
Q ss_pred cCCCCCCC
Q 030491 48 PCPYCYED 55 (176)
Q Consensus 48 ~CPFC~e~ 55 (176)
.||.||..
T Consensus 4 ~Cp~Cg~~ 11 (26)
T PF13248_consen 4 FCPNCGAE 11 (26)
T ss_pred CCcccCCc
Confidence 56777663
No 104
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=46.67 E-value=5.9 Score=30.24 Aligned_cols=13 Identities=15% Similarity=0.813 Sum_probs=11.3
Q ss_pred CCCCcccCCCCCC
Q 030491 42 DVRPDFPCPYCYE 54 (176)
Q Consensus 42 d~r~~F~CPFC~e 54 (176)
-+.+.|.|+|||+
T Consensus 32 ~Qhaky~CsfCGK 44 (92)
T KOG0402|consen 32 QQHAKYTCSFCGK 44 (92)
T ss_pred HHhhhhhhhhcch
Confidence 4578999999998
No 105
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.17 E-value=6.4 Score=30.21 Aligned_cols=30 Identities=20% Similarity=0.331 Sum_probs=21.0
Q ss_pred CCCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 42 d~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
+.+..+.|+-|+..|.+.. ....||-|-..
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 3467899999998665433 33459999754
No 106
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=45.80 E-value=9.6 Score=24.42 Aligned_cols=10 Identities=30% Similarity=0.657 Sum_probs=7.2
Q ss_pred ceecCccccc
Q 030491 75 VTVCPICSVK 84 (176)
Q Consensus 75 ~vVCPICaa~ 84 (176)
..+||.|-..
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 6788888653
No 107
>PRK11595 DNA utilization protein GntX; Provisional
Probab=45.77 E-value=10 Score=31.71 Aligned_cols=21 Identities=19% Similarity=0.325 Sum_probs=11.9
Q ss_pred cCCCCCCCCC--HHHHHhhhhhh
Q 030491 48 PCPYCYEDFD--IASLCSHLEDE 68 (176)
Q Consensus 48 ~CPFC~e~fD--v~~L~~H~~ee 68 (176)
.|+.|++.+. ...||..|.+.
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~ 29 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRA 29 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhh
Confidence 3777776432 23467777654
No 108
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=45.72 E-value=12 Score=34.36 Aligned_cols=41 Identities=29% Similarity=0.517 Sum_probs=30.7
Q ss_pred CCcccCCCCCCCCC--HHHHHhhhhhh-ccC-----CCcceecCccccc
Q 030491 44 RPDFPCPYCYEDFD--IASLCSHLEDE-HSC-----ESKVTVCPICSVK 84 (176)
Q Consensus 44 r~~F~CPFC~e~fD--v~~L~~H~~ee-H~~-----e~k~vVCPICaa~ 84 (176)
..+-.||.||...| +.+||.=|--+ |+. +.+..+|+-|-+.
T Consensus 4 ~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~ 52 (355)
T COG1499 4 ASTILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGAY 52 (355)
T ss_pred CcccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCCc
Confidence 34678999999887 88999888776 544 3345789999753
No 109
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.41 E-value=7.8 Score=30.26 Aligned_cols=36 Identities=25% Similarity=0.626 Sum_probs=22.6
Q ss_pred CcccCCCCCCCCCHH-H------HHhhhhhhccCCCcceecCccc
Q 030491 45 PDFPCPYCYEDFDIA-S------LCSHLEDEHSCESKVTVCPICS 82 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~-~------L~~H~~eeH~~e~k~vVCPICa 82 (176)
..+.||.|-+.|... . +|.-|...... ....||+|.
T Consensus 12 ~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~--~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLPCGHNFCRACLTRSWE--GPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcCccccccchHhHHHHHHhcC--CCcCCcccC
Confidence 478999998855554 2 23333333332 448999999
No 110
>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=45.24 E-value=20 Score=22.42 Aligned_cols=21 Identities=29% Similarity=0.585 Sum_probs=14.6
Q ss_pred cceecCcccccc-hhhHHHHhh
Q 030491 74 KVTVCPICSVKV-ARDMLSHIT 94 (176)
Q Consensus 74 k~vVCPICaa~~-s~d~l~HL~ 94 (176)
..+.||.|.-.+ ..-|..||-
T Consensus 3 ~~~~C~nC~R~v~a~RfA~HLe 24 (33)
T PF08209_consen 3 PYVECPNCGRPVAASRFAPHLE 24 (33)
T ss_dssp -EEE-TTTSSEEEGGGHHHHHH
T ss_pred CeEECCCCcCCcchhhhHHHHH
Confidence 357899998876 567888874
No 111
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=44.92 E-value=4.6 Score=30.76 Aligned_cols=35 Identities=23% Similarity=0.628 Sum_probs=22.3
Q ss_pred CCCCCCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 39 VEDDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 39 ~ddd~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.|..+++.+.||+|+.. .+ -+..+.--.|.-|-..
T Consensus 28 ie~~~~~~~~Cp~C~~~-~V----------kR~a~GIW~C~kCg~~ 62 (89)
T COG1997 28 IEAQQRAKHVCPFCGRT-TV----------KRIATGIWKCRKCGAK 62 (89)
T ss_pred HHHHHhcCCcCCCCCCc-ce----------eeeccCeEEcCCCCCe
Confidence 34467889999999873 11 1223444568877665
No 112
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=44.61 E-value=11 Score=26.94 Aligned_cols=26 Identities=35% Similarity=0.828 Sum_probs=16.8
Q ss_pred eecCcccccc--hhhHHHHhhhhccchh
Q 030491 76 TVCPICSVKV--ARDMLSHITLQHGHLF 101 (176)
Q Consensus 76 vVCPICaa~~--s~d~l~HL~~rH~~~~ 101 (176)
..||-|.+.. ..+.++|.+-.|+..+
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH~~~~ 45 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAHGWLF 45 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHhhhhh
Confidence 4555555543 5677777777787766
No 113
>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=44.37 E-value=20 Score=22.33 Aligned_cols=24 Identities=21% Similarity=0.551 Sum_probs=11.0
Q ss_pred cceecCcccccc------hhhHHHHhhhhc
Q 030491 74 KVTVCPICSVKV------ARDMLSHITLQH 97 (176)
Q Consensus 74 k~vVCPICaa~~------s~d~l~HL~~rH 97 (176)
..+.|-.|-..+ +.+|..||...|
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 345555554443 235566654443
No 114
>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=43.63 E-value=12 Score=35.71 Aligned_cols=48 Identities=33% Similarity=0.453 Sum_probs=33.7
Q ss_pred CCCHHHHHhhhhhhccCCC-----------------cceecCcccccc--hhhHHHHhhhhccchhh
Q 030491 55 DFDIASLCSHLEDEHSCES-----------------KVTVCPICSVKV--ARDMLSHITLQHGHLFK 102 (176)
Q Consensus 55 ~fDv~~L~~H~~eeH~~e~-----------------k~vVCPICaa~~--s~d~l~HL~~rH~~~~k 102 (176)
.+++..|..|+...|..+. +.-+||+|..+. ...+..|+...|-..++
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 4556666666666654222 245799999765 67999999999977663
No 115
>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=43.52 E-value=13 Score=23.95 Aligned_cols=10 Identities=40% Similarity=0.972 Sum_probs=8.2
Q ss_pred CcccCCCCCC
Q 030491 45 PDFPCPYCYE 54 (176)
Q Consensus 45 ~~F~CPFC~e 54 (176)
..|.||.||-
T Consensus 17 ~g~~CP~Cg~ 26 (46)
T PF12760_consen 17 DGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCC
Confidence 4689999985
No 116
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=42.25 E-value=13 Score=25.96 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=9.3
Q ss_pred CCcccCCCCCC
Q 030491 44 RPDFPCPYCYE 54 (176)
Q Consensus 44 r~~F~CPFC~e 54 (176)
+..|.||.||-
T Consensus 12 ~v~~~Cp~cGi 22 (55)
T PF13824_consen 12 HVNFECPDCGI 22 (55)
T ss_pred ccCCcCCCCCC
Confidence 56899999986
No 117
>PF14353 CpXC: CpXC protein
Probab=42.00 E-value=12 Score=28.52 Aligned_cols=30 Identities=27% Similarity=0.399 Sum_probs=19.0
Q ss_pred CCcccCCCCCCCCCHHHHHhhhhhhccCCCccee
Q 030491 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTV 77 (176)
Q Consensus 44 r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vV 77 (176)
-..|+||.||..+-+ .+--.+|-.+.+.++
T Consensus 36 l~~~~CP~Cg~~~~~----~~p~lY~D~~~~~~i 65 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRL----EYPLLYHDPEKKFMI 65 (128)
T ss_pred cCEEECCCCCCceec----CCCEEEEcCCCCEEE
Confidence 357999999996543 344455555555433
No 118
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=41.96 E-value=15 Score=32.54 Aligned_cols=51 Identities=24% Similarity=0.493 Sum_probs=24.1
Q ss_pred ccCCCCCCCC-CHHHHHhhhhhhccCCCcceecCcccccch--hhHHHHhhhhccc
Q 030491 47 FPCPYCYEDF-DIASLCSHLEDEHSCESKVTVCPICSVKVA--RDMLSHITLQHGH 99 (176)
Q Consensus 47 F~CPFC~e~f-Dv~~L~~H~~eeH~~e~k~vVCPICaa~~s--~d~l~HL~~rH~~ 99 (176)
+.|-|||++| |.-+|-.|.... ..-++..|.+|-.-.+ -.+-.||.--||.
T Consensus 146 ~lct~cgkgfndtfdlkrh~rth--tgvrpykc~~c~kaftqrcsleshl~kvhgv 199 (267)
T KOG3576|consen 146 HLCTFCGKGFNDTFDLKRHTRTH--TGVRPYKCSLCEKAFTQRCSLESHLKKVHGV 199 (267)
T ss_pred HHHhhccCcccchhhhhhhhccc--cCccccchhhhhHHHHhhccHHHHHHHHcCc
Confidence 3344444432 223344444433 3344555666655432 2556677655553
No 119
>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=41.84 E-value=11 Score=29.13 Aligned_cols=38 Identities=26% Similarity=0.531 Sum_probs=21.2
Q ss_pred ccCCCCCCCCCHHHHHhhhhhh-ccC-CCc-ceecCcccccchh
Q 030491 47 FPCPYCYEDFDIASLCSHLEDE-HSC-ESK-VTVCPICSVKVAR 87 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~ee-H~~-e~k-~vVCPICaa~~s~ 87 (176)
-.|||||....+ ...-+.+ |.. +.. .-+|+-|-+.|+-
T Consensus 3 ~~CpYCg~~~~l---~~~~~iYg~~~~~~~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAEL---VDGSEIYGHRYDDGPYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEE---cccchhcCccCCCCceeEECCCCCceeee
Confidence 369999883222 1222222 222 122 3799999999753
No 120
>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=41.38 E-value=2.4 Score=25.91 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=4.5
Q ss_pred CcceecCcc
Q 030491 73 SKVTVCPIC 81 (176)
Q Consensus 73 ~k~vVCPIC 81 (176)
...+.||+|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 344456655
No 121
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=41.31 E-value=32 Score=32.67 Aligned_cols=48 Identities=27% Similarity=0.538 Sum_probs=29.6
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccc--hhhHHHHhh
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHIT 94 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~--s~d~l~HL~ 94 (176)
.|.||.|+- ==..++|-.|+...|.- .+.-.|--|...- -.|+..|+.
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhhhccHHHHHHHHH
Confidence 577777776 33456777777777765 6666777776652 234444443
No 122
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=41.25 E-value=16 Score=23.78 Aligned_cols=26 Identities=27% Similarity=0.589 Sum_probs=14.6
Q ss_pred CcccCCCCCCCCCHH------HHHhhhhhhcc
Q 030491 45 PDFPCPYCYEDFDIA------SLCSHLEDEHS 70 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~------~L~~H~~eeH~ 70 (176)
+.-.|-+|+..+... .|..|+...|+
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 456677776644332 56666655544
No 123
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.04 E-value=8.6 Score=30.37 Aligned_cols=18 Identities=11% Similarity=0.497 Sum_probs=13.4
Q ss_pred CCCCcccCCCCCCCCCHH
Q 030491 42 DVRPDFPCPYCYEDFDIA 59 (176)
Q Consensus 42 d~r~~F~CPFC~e~fDv~ 59 (176)
..+..+.|+-||..+...
T Consensus 66 ~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred ecceEEECCCCCCEEecc
Confidence 346789999999855543
No 124
>PHA00733 hypothetical protein
Probab=40.21 E-value=28 Score=27.26 Aligned_cols=25 Identities=24% Similarity=0.388 Sum_probs=21.8
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhcc
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHS 70 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~ 70 (176)
.|.|+.|++ --....|..|....|.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 599999999 4566889999999996
No 125
>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=40.04 E-value=20 Score=28.94 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=14.7
Q ss_pred CcccCCCCCC---CCCHHHHHhhh
Q 030491 45 PDFPCPYCYE---DFDIASLCSHL 65 (176)
Q Consensus 45 ~~F~CPFC~e---~fDv~~L~~H~ 65 (176)
..|.||-||. .+|-..+..=+
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i~~l 150 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAIEKL 150 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHHHHH
Confidence 4799999998 55655555433
No 126
>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=39.51 E-value=12 Score=28.62 Aligned_cols=19 Identities=21% Similarity=0.627 Sum_probs=12.8
Q ss_pred CcccCCCCCC-CCCHHHHHh
Q 030491 45 PDFPCPYCYE-DFDIASLCS 63 (176)
Q Consensus 45 ~~F~CPFC~e-~fDv~~L~~ 63 (176)
..|.||+|.. .=.+..+..
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~~ 42 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWVK 42 (178)
T ss_pred ECCCCcchhhhhHHHHHHHH
Confidence 4699999988 544444444
No 127
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=39.17 E-value=12 Score=26.88 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=22.9
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccC
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSC 71 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~ 71 (176)
-|.||-||. =-+..+...|++..|-.
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 789999999 66788999999999875
No 128
>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=39.04 E-value=12 Score=29.93 Aligned_cols=41 Identities=20% Similarity=0.566 Sum_probs=28.8
Q ss_pred CcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccchhhHH
Q 030491 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~d~l 90 (176)
..+.|.-|+..++...+........ ...||.|...+..|++
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 3589999999888777766554442 2399999987655543
No 129
>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=38.99 E-value=6.2 Score=29.70 Aligned_cols=38 Identities=29% Similarity=0.679 Sum_probs=12.8
Q ss_pred cCCCCCCCCCHHHHH-hhhhhhccC-----------CCcceecCcccccc
Q 030491 48 PCPYCYEDFDIASLC-SHLEDEHSC-----------ESKVTVCPICSVKV 85 (176)
Q Consensus 48 ~CPFC~e~fDv~~L~-~H~~eeH~~-----------e~k~vVCPICaa~~ 85 (176)
.||+|++.+...++. .=|..-|.. +++.-+|++|..+.
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 699999977766643 447777865 55668899998764
No 130
>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=38.91 E-value=4.3 Score=30.99 Aligned_cols=29 Identities=24% Similarity=0.544 Sum_probs=18.0
Q ss_pred CCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 43 ~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.+..+.|+-||..|+..... ..||-|-..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~-------------~~CP~Cgs~ 95 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD-------------FSCPRCGSP 95 (113)
T ss_dssp E--EEEETTTS-EEECHHCC-------------HH-SSSSSS
T ss_pred cCCcEECCCCCCEEecCCCC-------------CCCcCCcCC
Confidence 46789999999977665433 229999765
No 131
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=38.72 E-value=18 Score=31.86 Aligned_cols=37 Identities=22% Similarity=0.604 Sum_probs=26.6
Q ss_pred CcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccchhhHHHH
Q 030491 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSH 92 (176)
Q Consensus 45 ~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~d~l~H 92 (176)
....||.||. ++ +.+ .+...+||.-|-..+..+++.+
T Consensus 10 ~~~~Cp~Cg~~~i--------v~d---~~~Ge~vC~~CG~Vl~e~~iD~ 47 (310)
T PRK00423 10 EKLVCPECGSDKL--------IYD---YERGEIVCADCGLVIEENIIDQ 47 (310)
T ss_pred cCCcCcCCCCCCe--------eEE---CCCCeEeecccCCccccccccc
Confidence 3467999996 22 112 3577899999999988877653
No 132
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=38.71 E-value=26 Score=33.27 Aligned_cols=43 Identities=16% Similarity=0.408 Sum_probs=27.5
Q ss_pred HHHHhhhhhhc-cCCCcceecCcccccc--hhhHHHHhhhhccchh
Q 030491 59 ASLCSHLEDEH-SCESKVTVCPICSVKV--ARDMLSHITLQHGHLF 101 (176)
Q Consensus 59 ~~L~~H~~eeH-~~e~k~vVCPICaa~~--s~d~l~HL~~rH~~~~ 101 (176)
..+..|..+.| .+.+....|-+|...- +.++..||+-+|+|-.
T Consensus 335 ~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~ 380 (467)
T KOG3608|consen 335 TQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRL 380 (467)
T ss_pred HHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccC
Confidence 44455555555 2334445677776543 6799999999999843
No 133
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=38.71 E-value=21 Score=24.67 Aligned_cols=39 Identities=23% Similarity=0.424 Sum_probs=24.7
Q ss_pred CcccCCCCCCCCCHHHHHhhh-----------------hhhccCCCcceecCcccc
Q 030491 45 PDFPCPYCYEDFDIASLCSHL-----------------EDEHSCESKVTVCPICSV 83 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~-----------------~eeH~~e~k~vVCPICaa 83 (176)
....||+|.-.+|-..|+.=. --+........+||.|..
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 367899997788777776622 222233446789999954
No 134
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=38.46 E-value=16 Score=25.58 Aligned_cols=13 Identities=31% Similarity=0.874 Sum_probs=9.4
Q ss_pred cccCCCCCCCCCH
Q 030491 46 DFPCPYCYEDFDI 58 (176)
Q Consensus 46 ~F~CPFC~e~fDv 58 (176)
.=-||||+.-|+-
T Consensus 39 YngCPfC~~~~~~ 51 (55)
T PF14447_consen 39 YNGCPFCGTPFEF 51 (55)
T ss_pred ccCCCCCCCcccC
Confidence 4469999986653
No 135
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=38.30 E-value=32 Score=21.46 Aligned_cols=31 Identities=19% Similarity=0.591 Sum_probs=18.0
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccc
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa 83 (176)
+.||-|+..|++.+- .=+.....|-||.|..
T Consensus 3 i~Cp~C~~~y~i~d~------~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDE------KIPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHH------HCCCCCcEEECCCCCC
Confidence 568888774444321 1123455778888854
No 136
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=37.11 E-value=12 Score=35.64 Aligned_cols=17 Identities=29% Similarity=0.677 Sum_probs=13.8
Q ss_pred cCCCcceecCcccccch
Q 030491 70 SCESKVTVCPICSVKVA 86 (176)
Q Consensus 70 ~~e~k~vVCPICaa~~s 86 (176)
..+++.-|||||...||
T Consensus 32 ~~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 32 GAEPNTNVCPVCLGLPG 48 (474)
T ss_pred CCCCCCCcCccccCCCC
Confidence 34678899999999973
No 137
>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=37.11 E-value=15 Score=28.92 Aligned_cols=12 Identities=25% Similarity=0.767 Sum_probs=7.2
Q ss_pred CcceecCccccc
Q 030491 73 SKVTVCPICSVK 84 (176)
Q Consensus 73 ~k~vVCPICaa~ 84 (176)
....|||-|+--
T Consensus 17 g~~~iCpeC~~E 28 (109)
T TIGR00686 17 GTQLICPSCLYE 28 (109)
T ss_pred CCeeECcccccc
Confidence 445677777653
No 138
>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=37.10 E-value=15 Score=27.56 Aligned_cols=8 Identities=63% Similarity=1.767 Sum_probs=5.8
Q ss_pred ccCCCCCC
Q 030491 47 FPCPYCYE 54 (176)
Q Consensus 47 F~CPFC~e 54 (176)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 46888874
No 139
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=36.68 E-value=12 Score=31.48 Aligned_cols=38 Identities=26% Similarity=0.424 Sum_probs=0.0
Q ss_pred ceecCcccccc-hhhHHHHhhhhccc-hhhhhhccccccc
Q 030491 75 VTVCPICSVKV-ARDMLSHITLQHGH-LFKLQRRRRLRRV 112 (176)
Q Consensus 75 ~vVCPICaa~~-s~d~l~HL~~rH~~-~~k~~r~rr~rr~ 112 (176)
.++||||-.+| ...|-.||.+.=-- -||-+|.+-..|.
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 37999999985 67899998754322 2444455544443
No 140
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.32 E-value=17 Score=30.46 Aligned_cols=30 Identities=30% Similarity=0.652 Sum_probs=22.2
Q ss_pred CCcccCCCCCC--CCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 44 RPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 44 r~~F~CPFC~e--~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
..-|.||-|.. .||.+-+.. -.||.|-+.+
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~~~------------F~Cp~Cg~~L 142 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAMELG------------FTCPKCGEDL 142 (176)
T ss_pred CCceeCCCCCCcccHHHHHHhC------------CCCCCCCchh
Confidence 35799999988 555554433 6899998875
No 141
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=36.27 E-value=12 Score=31.42 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=0.0
Q ss_pred cccCCCCCCCCCHHHHHhhhhhh
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDE 68 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~ee 68 (176)
...||+||+-+-+..+-+|+.-.
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi~ 190 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRIE 190 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 48999999999999999998754
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=36.24 E-value=24 Score=28.50 Aligned_cols=32 Identities=19% Similarity=0.359 Sum_probs=22.9
Q ss_pred CCCCcccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccch
Q 030491 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (176)
Q Consensus 42 d~r~~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s 86 (176)
++-....||-||. =+|+ ...++|||-|-....
T Consensus 5 elGtKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDL-------------NRRPAVSPYTGEQFP 37 (129)
T ss_pred hhCccccCCCcCcccccc-------------CCCCccCCCcCCccC
Confidence 3456789999998 4442 346899999987643
No 143
>PF14968 CCDC84: Coiled coil protein 84
Probab=35.82 E-value=19 Score=33.12 Aligned_cols=18 Identities=22% Similarity=0.477 Sum_probs=14.1
Q ss_pred CCCCcccCCCCCCCCCHH
Q 030491 42 DVRPDFPCPYCYEDFDIA 59 (176)
Q Consensus 42 d~r~~F~CPFC~e~fDv~ 59 (176)
+-+..|=|+||+.++...
T Consensus 54 ~~~~~fWC~fC~~ev~~~ 71 (336)
T PF14968_consen 54 EHRNRFWCVFCDCEVREH 71 (336)
T ss_pred cccceeEeeCccchhhhc
Confidence 557799999998876644
No 144
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.77 E-value=15 Score=38.46 Aligned_cols=36 Identities=19% Similarity=0.405 Sum_probs=16.2
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
.|.||.||+.-...--|..|.. ......||-|-..+
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 3555555553233334444422 12234466665553
No 145
>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=35.55 E-value=13 Score=26.39 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=8.4
Q ss_pred CCcccCCCCCC
Q 030491 44 RPDFPCPYCYE 54 (176)
Q Consensus 44 r~~F~CPFC~e 54 (176)
...+.|-+||+
T Consensus 3 k~~~~C~~Cg~ 13 (69)
T PF09706_consen 3 KKKYNCIFCGE 13 (69)
T ss_pred CCCCcCcCCCC
Confidence 34788999994
No 146
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.32 E-value=20 Score=25.71 Aligned_cols=13 Identities=38% Similarity=0.976 Sum_probs=8.3
Q ss_pred CCcceecCccccc
Q 030491 72 ESKVTVCPICSVK 84 (176)
Q Consensus 72 e~k~vVCPICaa~ 84 (176)
+...|+||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 5556777777654
No 147
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=34.07 E-value=28 Score=28.73 Aligned_cols=19 Identities=37% Similarity=0.800 Sum_probs=13.3
Q ss_pred CcccCCCCCC---CCCHHHHHh
Q 030491 45 PDFPCPYCYE---DFDIASLCS 63 (176)
Q Consensus 45 ~~F~CPFC~e---~fDv~~L~~ 63 (176)
..|.||.||. .+|-..+..
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~ 156 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIK 156 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHH
Confidence 4799999998 555444443
No 148
>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=33.70 E-value=3.7 Score=30.78 Aligned_cols=21 Identities=29% Similarity=0.641 Sum_probs=16.4
Q ss_pred CcccCCCCCC-CCCHHHHHhhh
Q 030491 45 PDFPCPYCYE-DFDIASLCSHL 65 (176)
Q Consensus 45 ~~F~CPFC~e-~fDv~~L~~H~ 65 (176)
..|.||+|.. .-.+..|..+.
T Consensus 20 ~d~~Cp~C~~~~~~~~~~~~~~ 41 (162)
T PF13462_consen 20 FDFQCPHCAKFHEELEKLLKKY 41 (162)
T ss_dssp E-TTSHHHHHHHHHHHHHHHHH
T ss_pred ECCCCHhHHHHHHHHhhhhhhc
Confidence 4699999998 77777888775
No 149
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.62 E-value=23 Score=33.34 Aligned_cols=16 Identities=31% Similarity=0.756 Sum_probs=11.4
Q ss_pred CCcccCCCCCCCCCHH
Q 030491 44 RPDFPCPYCYEDFDIA 59 (176)
Q Consensus 44 r~~F~CPFC~e~fDv~ 59 (176)
..+|.||||..+-+..
T Consensus 372 ~~sfKCPYCP~e~~~~ 387 (394)
T KOG2817|consen 372 SQSFKCPYCPVEQLAS 387 (394)
T ss_pred CeeeeCCCCCcccCHH
Confidence 3469999998755443
No 150
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=33.55 E-value=34 Score=25.80 Aligned_cols=36 Identities=25% Similarity=0.555 Sum_probs=26.5
Q ss_pred ccCCCCCC-----CCCHHHHHhhhhhhccC------CCcceecCcccc
Q 030491 47 FPCPYCYE-----DFDIASLCSHLEDEHSC------ESKVTVCPICSV 83 (176)
Q Consensus 47 F~CPFC~e-----~fDv~~L~~H~~eeH~~------e~k~vVCPICaa 83 (176)
=.||-|-. .+ +-++|.|+--.|+. .++.+-||.|..
T Consensus 32 g~Cp~Ck~PgDdCPL-v~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq 78 (84)
T KOG1493|consen 32 GCCPDCKLPGDDCPL-VWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQ 78 (84)
T ss_pred CcCCCCcCCCCCCcc-HHHHHHHHHHHHHHHHHhcCccccccCCcchh
Confidence 36788833 34 77899999888874 455689999964
No 151
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=33.42 E-value=25 Score=19.15 Aligned_cols=16 Identities=25% Similarity=0.752 Sum_probs=7.4
Q ss_pred cCcccccc--hhhHHHHh
Q 030491 78 CPICSVKV--ARDMLSHI 93 (176)
Q Consensus 78 CPICaa~~--s~d~l~HL 93 (176)
|.||-... ...|..|+
T Consensus 3 C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQHL 20 (25)
T ss_dssp ETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCcCCHHHHHHHH
Confidence 55554433 23445554
No 152
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.34 E-value=13 Score=32.58 Aligned_cols=43 Identities=26% Similarity=0.574 Sum_probs=30.7
Q ss_pred CCcccCCCCCC--CCCHHHHHhhhh-------hhccCCCcceecCcccccchh
Q 030491 44 RPDFPCPYCYE--DFDIASLCSHLE-------DEHSCESKVTVCPICSVKVAR 87 (176)
Q Consensus 44 r~~F~CPFC~e--~fDv~~L~~H~~-------eeH~~e~k~vVCPICaa~~s~ 87 (176)
-..|.|-.|.+ .==|..||-|+- --| .......||||-+.|+.
T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~-~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQ-TRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccccCCCEEeecccceehHHHHHHHh-hcCCCeeCCcccccccc
Confidence 35799999987 555788998863 111 13456789999998754
No 153
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.97 E-value=13 Score=33.79 Aligned_cols=41 Identities=27% Similarity=0.536 Sum_probs=25.6
Q ss_pred CcccCCCCCC--CCCHHHH-HhhhhhhccCCCcc-----eecCcccccc
Q 030491 45 PDFPCPYCYE--DFDIASL-CSHLEDEHSCESKV-----TVCPICSVKV 85 (176)
Q Consensus 45 ~~F~CPFC~e--~fDv~~L-~~H~~eeH~~e~k~-----vVCPICaa~~ 85 (176)
.+-.||+||+ -+--... |.|+-=+-+.-++. -.||-|.+.+
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 4678999999 3433444 88855444443332 3788887654
No 154
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=32.83 E-value=15 Score=35.63 Aligned_cols=20 Identities=30% Similarity=0.552 Sum_probs=15.9
Q ss_pred hhccCCCcceecCcccccch
Q 030491 67 DEHSCESKVTVCPICSVKVA 86 (176)
Q Consensus 67 eeH~~e~k~vVCPICaa~~s 86 (176)
.+...+++.-|||||...|+
T Consensus 85 ~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 85 YNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred cccCCCCccCcCccccCCCC
Confidence 34455889999999999973
No 155
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.31 E-value=14 Score=28.45 Aligned_cols=31 Identities=29% Similarity=0.612 Sum_probs=21.1
Q ss_pred CCCCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 42 d~r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
+.+..+.|+-||..|..... ....||-|...
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 34678999999986655422 22459999764
No 156
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=32.22 E-value=17 Score=24.67 Aligned_cols=44 Identities=23% Similarity=0.554 Sum_probs=28.6
Q ss_pred CCCCCCCC-CCCCcccCCCCCC--CCCHHHHHhhhhhhccCCCcceecCcccccch
Q 030491 34 IDDFEVED-DVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (176)
Q Consensus 34 ~d~~~~dd-d~r~~F~CPFC~e--~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s 86 (176)
+||++.++ +..-.|+|+ ||. .++...|-++ .-.|.|+-|+-.+.
T Consensus 5 l~d~~~~~~~~~~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 5 LDDMEFDEEEGVYSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIR 51 (55)
T ss_dssp TTTSEEETTTTEEEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEE
T ss_pred hhhceecCCCCEEEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEE
Confidence 45544332 234689995 988 7777777666 44678999987653
No 157
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.87 E-value=9.6 Score=35.17 Aligned_cols=40 Identities=25% Similarity=0.581 Sum_probs=31.2
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCC---------CcceecCcccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCE---------SKVTVCPICSVKV 85 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e---------~k~vVCPICaa~~ 85 (176)
++.|-.|-|+|...+.+.++-=.|.+- ...-.||||-..+
T Consensus 229 ~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 229 TDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred CceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 399999999998888887777777762 2346799998765
No 158
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.55 E-value=8.9 Score=30.13 Aligned_cols=22 Identities=27% Similarity=0.889 Sum_probs=15.2
Q ss_pred CCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 49 CPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 49 CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
||.||..+-+. ...||-|...+
T Consensus 1 CPvCg~~l~vt---------------~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVT---------------RLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEE---------------EEEcCCCCCEE
Confidence 89998876554 45677776664
No 159
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=31.48 E-value=24 Score=29.66 Aligned_cols=13 Identities=46% Similarity=0.958 Sum_probs=10.2
Q ss_pred ccCCCCCCCCCHH
Q 030491 47 FPCPYCYEDFDIA 59 (176)
Q Consensus 47 F~CPFC~e~fDv~ 59 (176)
=+||+||.-+|-.
T Consensus 155 P~CPlCg~PlDP~ 167 (171)
T PF11290_consen 155 PPCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCCC
Confidence 4799999977743
No 160
>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=31.16 E-value=12 Score=27.96 Aligned_cols=7 Identities=57% Similarity=1.497 Sum_probs=4.3
Q ss_pred cCCCCCC
Q 030491 48 PCPYCYE 54 (176)
Q Consensus 48 ~CPFC~e 54 (176)
+|||||+
T Consensus 3 ~CP~CG~ 9 (84)
T PF04267_consen 3 PCPHCGP 9 (84)
T ss_dssp EETTTEE
T ss_pred cCCCCCc
Confidence 5666665
No 161
>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=30.85 E-value=19 Score=23.48 Aligned_cols=9 Identities=44% Similarity=1.180 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 030491 46 DFPCPYCYE 54 (176)
Q Consensus 46 ~F~CPFC~e 54 (176)
.-.||||+.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 578999985
No 162
>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=30.81 E-value=13 Score=24.54 Aligned_cols=17 Identities=41% Similarity=0.960 Sum_probs=11.1
Q ss_pred cccCCCCCC-CCCHHHHH
Q 030491 46 DFPCPYCYE-DFDIASLC 62 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~ 62 (176)
.|.||+|.. .-.+..+.
T Consensus 6 d~~Cp~C~~~~~~l~~~~ 23 (98)
T cd02972 6 DPLCPYCYLFEPELEKLL 23 (98)
T ss_pred CCCCHhHHhhhHHHHHHH
Confidence 578999988 44444443
No 163
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=30.57 E-value=38 Score=28.41 Aligned_cols=38 Identities=16% Similarity=0.382 Sum_probs=24.3
Q ss_pred ccCCCCCC---CCCHHHHHhhhhhhccCC-CcceecCccccc
Q 030491 47 FPCPYCYE---DFDIASLCSHLEDEHSCE-SKVTVCPICSVK 84 (176)
Q Consensus 47 F~CPFC~e---~fDv~~L~~H~~eeH~~e-~k~vVCPICaa~ 84 (176)
=.||+|+. .++..+-..-+...|... ...-+||.|-..
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 36999976 555555555555555543 335779999776
No 164
>PF14369 zf-RING_3: zinc-finger
Probab=30.51 E-value=24 Score=22.06 Aligned_cols=9 Identities=44% Similarity=1.228 Sum_probs=7.7
Q ss_pred cCCCCCCCC
Q 030491 48 PCPYCYEDF 56 (176)
Q Consensus 48 ~CPFC~e~f 56 (176)
.||.|+.+|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 799998766
No 165
>PHA02929 N1R/p28-like protein; Provisional
Probab=30.37 E-value=10 Score=33.08 Aligned_cols=41 Identities=24% Similarity=0.514 Sum_probs=23.4
Q ss_pred CcccCCCCCCCCCHH----------HHHhhhhhhccC---CCcceecCcccccc
Q 030491 45 PDFPCPYCYEDFDIA----------SLCSHLEDEHSC---ESKVTVCPICSVKV 85 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~----------~L~~H~~eeH~~---e~k~vVCPICaa~~ 85 (176)
....||.|.+.+... .=|.|.--..+. -.....||+|...+
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~ 226 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF 226 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence 467999998865432 124543222211 12356899998764
No 166
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=30.29 E-value=32 Score=30.45 Aligned_cols=55 Identities=29% Similarity=0.544 Sum_probs=43.8
Q ss_pred cccCCCCCCCCCHH-HHHhhhhhhccCC---------CcceecCcccccc--hhhHHHHhhhhccch
Q 030491 46 DFPCPYCYEDFDIA-SLCSHLEDEHSCE---------SKVTVCPICSVKV--ARDMLSHITLQHGHL 100 (176)
Q Consensus 46 ~F~CPFC~e~fDv~-~L~~H~~eeH~~e---------~k~vVCPICaa~~--s~d~l~HL~~rH~~~ 100 (176)
-|.|-.|++.|.+. +|-.|+..-|... .+..||--|...- -...+.|+...|.++
T Consensus 173 pykc~~c~kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 173 PYKCSLCEKAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred ccchhhhhHHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCC
Confidence 59999999987764 8999999999863 3458999997653 457888999888764
No 167
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.11 E-value=34 Score=34.21 Aligned_cols=28 Identities=32% Similarity=0.500 Sum_probs=24.9
Q ss_pred CCcccCCCCCC-CCCHHHHHhhhhhhccC
Q 030491 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSC 71 (176)
Q Consensus 44 r~~F~CPFC~e-~fDv~~L~~H~~eeH~~ 71 (176)
+.--.|+||-+ -||..+|..|+..+|.+
T Consensus 180 rGhp~C~~C~~~fld~~el~rH~~~~h~~ 208 (669)
T KOG2231|consen 180 RGHPLCKFCHERFLDDDELYRHLRFDHEF 208 (669)
T ss_pred cCCccchhhhhhhccHHHHHHhhccceeh
Confidence 44678999999 99999999999999986
No 168
>TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit. The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both.
Probab=29.97 E-value=19 Score=34.41 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=13.3
Q ss_pred CCcceecCcccccch
Q 030491 72 ESKVTVCPICSVKVA 86 (176)
Q Consensus 72 e~k~vVCPICaa~~s 86 (176)
+++.-|||||...||
T Consensus 34 ~PNt~v~pvclg~PG 48 (478)
T TIGR00133 34 PPNTNVCPVCLGLPG 48 (478)
T ss_pred CCCcccCccccCCCC
Confidence 788999999999973
No 169
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=29.95 E-value=20 Score=38.37 Aligned_cols=35 Identities=31% Similarity=0.737 Sum_probs=19.1
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
.|.||-||. .+. ..|..|-.. .++ ..+||.|-+.+
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~--te~-vy~CPsCGaev 702 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTH--TEP-VYVCPDCGAEV 702 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCc--CCC-ceeCccCCCcc
Confidence 578888887 332 355555543 111 23666666653
No 170
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=29.79 E-value=17 Score=33.14 Aligned_cols=18 Identities=22% Similarity=0.615 Sum_probs=13.8
Q ss_pred cceecCcccccchhhHHH
Q 030491 74 KVTVCPICSVKVARDMLS 91 (176)
Q Consensus 74 k~vVCPICaa~~s~d~l~ 91 (176)
+..+||||..+|...|+.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 457999999998666653
No 171
>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=29.76 E-value=13 Score=27.55 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=18.0
Q ss_pred CCCCCCCCCHHHHHhhhhhhcc----CCCcceecCcccccc
Q 030491 49 CPYCYEDFDIASLCSHLEDEHS----CESKVTVCPICSVKV 85 (176)
Q Consensus 49 CPFC~e~fDv~~L~~H~~eeH~----~e~k~vVCPICaa~~ 85 (176)
||+|+.+--+.....+.-+.-. .+....+||.|-...
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 8999863222333332211100 122345699997763
No 172
>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=29.62 E-value=24 Score=33.80 Aligned_cols=42 Identities=29% Similarity=0.585 Sum_probs=26.6
Q ss_pred CCcccCCCCCCCCCHHHHHhhhhhh--ccCCCcceecCcccccchh
Q 030491 44 RPDFPCPYCYEDFDIASLCSHLEDE--HSCESKVTVCPICSVKVAR 87 (176)
Q Consensus 44 r~~F~CPFC~e~fDv~~L~~H~~ee--H~~e~k~vVCPICaa~~s~ 87 (176)
+-..+||-||+.+... .+++.-+ ...+.-..+||-|-..+..
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 4568999999944433 1222222 1344556899999998854
No 173
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=28.53 E-value=35 Score=23.93 Aligned_cols=44 Identities=25% Similarity=0.532 Sum_probs=21.1
Q ss_pred CCCcccCC--CCCCCCCHHHHHhhhhhhccC----CCcceecCcccccch
Q 030491 43 VRPDFPCP--YCYEDFDIASLCSHLEDEHSC----ESKVTVCPICSVKVA 86 (176)
Q Consensus 43 ~r~~F~CP--FC~e~fDv~~L~~H~~eeH~~----e~k~vVCPICaa~~s 86 (176)
..+...|| -|+.-|-..=|.+........ ....+.||.|...++
T Consensus 17 ~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 17 EIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp ----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 34568887 888888888888887765443 345577999998764
No 174
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.35 E-value=37 Score=31.58 Aligned_cols=24 Identities=29% Similarity=0.847 Sum_probs=20.2
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhcc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHS 70 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~ 70 (176)
+.-||||.-.+...+.|.|++ .|-
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 357999988999999999999 443
No 175
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=28.29 E-value=27 Score=25.33 Aligned_cols=8 Identities=50% Similarity=1.464 Sum_probs=6.3
Q ss_pred ccCCCCCC
Q 030491 47 FPCPYCYE 54 (176)
Q Consensus 47 F~CPFC~e 54 (176)
|.||+||.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 57888877
No 176
>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=28.10 E-value=17 Score=34.34 Aligned_cols=32 Identities=38% Similarity=1.001 Sum_probs=14.9
Q ss_pred CcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcc-cccchhhH
Q 030491 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPIC-SVKVARDM 89 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPIC-aa~~s~d~ 89 (176)
+.-.|||||..+ |+ +-+--+|||| .+.++.+-
T Consensus 379 ~~v~CP~cgA~y------------~~-~~kG~lC~vC~l~~IG~~a 411 (422)
T PF06957_consen 379 PSVKCPYCGAKY------------HP-EYKGQLCPVCELSEIGADA 411 (422)
T ss_dssp -EEE-TTT--EE------------EG-GGTTSB-TTTTTBBTT---
T ss_pred CCeeCCCCCCcc------------Ch-hhCCCCCCCCcceeeCCcc
Confidence 346799998633 21 2345699999 44666543
No 177
>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=27.88 E-value=14 Score=33.77 Aligned_cols=39 Identities=28% Similarity=0.486 Sum_probs=26.1
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhcc-CCCcceecCcccccc
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHS-CESKVTVCPICSVKV 85 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~-~e~k~vVCPICaa~~ 85 (176)
=.||+|+-+---...|+.|-.... .+-.+.+|.+|...+
T Consensus 137 g~CP~C~~~~a~g~~Ce~cG~~~~~~~l~~p~~~~~g~~~ 176 (391)
T PF09334_consen 137 GTCPYCGSDKARGDQCENCGRPLEPEELINPVCKICGSPP 176 (391)
T ss_dssp CEETTT--SSCTTTEETTTSSBEECCCSECEEETTTS-B-
T ss_pred ccccCcCccccCCCcccCCCCCcccccccCCccccccccC
Confidence 569999865555567777766544 577889999998875
No 178
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=27.85 E-value=21 Score=36.78 Aligned_cols=49 Identities=16% Similarity=0.377 Sum_probs=39.4
Q ss_pred ccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCcccccc--hhhHHHHhhhhc
Q 030491 47 FPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQH 97 (176)
Q Consensus 47 F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~--s~d~l~HL~~rH 97 (176)
-.|-||++ .=....|.-|+... ...+..+|-||..+. ..|+-.|+...|
T Consensus 354 hkCr~CakvfgS~SaLqiHlRSH--TGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 354 HKCRFCAKVFGSDSALQIHLRSH--TGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred chhhhhHhhcCchhhhhhhhhcc--CCCCCeeecccccccccccceeeeeeecc
Confidence 45999999 66788999999876 667889999999886 458888875433
No 179
>PRK10220 hypothetical protein; Provisional
Probab=27.45 E-value=42 Score=26.55 Aligned_cols=10 Identities=30% Similarity=0.956 Sum_probs=6.0
Q ss_pred cceecCcccc
Q 030491 74 KVTVCPICSV 83 (176)
Q Consensus 74 k~vVCPICaa 83 (176)
...|||-|+-
T Consensus 19 ~~~vCpeC~h 28 (111)
T PRK10220 19 GMYICPECAH 28 (111)
T ss_pred CeEECCcccC
Confidence 3466666654
No 180
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=27.29 E-value=27 Score=32.60 Aligned_cols=11 Identities=55% Similarity=1.256 Sum_probs=9.2
Q ss_pred CCcccCCCCCC
Q 030491 44 RPDFPCPYCYE 54 (176)
Q Consensus 44 r~~F~CPFC~e 54 (176)
..+|.||||.+
T Consensus 374 ~~~FKCPYCP~ 384 (396)
T COG5109 374 VLSFKCPYCPE 384 (396)
T ss_pred cEEeeCCCCCc
Confidence 34799999987
No 181
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=27.23 E-value=19 Score=27.66 Aligned_cols=11 Identities=18% Similarity=0.552 Sum_probs=5.8
Q ss_pred CCcccCCCCCC
Q 030491 44 RPDFPCPYCYE 54 (176)
Q Consensus 44 r~~F~CPFC~e 54 (176)
+..+.|+-|+.
T Consensus 68 p~~~~C~~Cg~ 78 (114)
T PRK03681 68 EAECWCETCQQ 78 (114)
T ss_pred CcEEEcccCCC
Confidence 44555555555
No 182
>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=26.86 E-value=37 Score=21.00 Aligned_cols=12 Identities=25% Similarity=0.562 Sum_probs=8.2
Q ss_pred CCCcccCCCCCC
Q 030491 43 VRPDFPCPYCYE 54 (176)
Q Consensus 43 ~r~~F~CPFC~e 54 (176)
......||+||-
T Consensus 14 ~~~~irC~~CG~ 25 (32)
T PF03604_consen 14 PGDPIRCPECGH 25 (32)
T ss_dssp TSSTSSBSSSS-
T ss_pred CCCcEECCcCCC
Confidence 345678999974
No 183
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=26.59 E-value=21 Score=29.76 Aligned_cols=40 Identities=23% Similarity=0.558 Sum_probs=25.6
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhc-----cCCC-cceecCcccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEH-----SCES-KVTVCPICSVKV 85 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH-----~~e~-k~vVCPICaa~~ 85 (176)
-=.||.|+..++...-..|++=.| .... +-+.|+-|-...
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 347999999776432223777777 3332 456799997653
No 184
>PHA02540 61 DNA primase; Provisional
Probab=26.09 E-value=29 Score=31.70 Aligned_cols=24 Identities=17% Similarity=0.348 Sum_probs=14.6
Q ss_pred cCcccccchhhHHHHhhhhccchhhh
Q 030491 78 CPICSVKVARDMLSHITLQHGHLFKL 103 (176)
Q Consensus 78 CPICaa~~s~d~l~HL~~rH~~~~k~ 103 (176)
|=-|-+ +.|++.-++-..+.+|.-
T Consensus 58 CFgCGa--~Gd~i~Flme~e~lsf~E 81 (337)
T PHA02540 58 CHNCGY--HRPFGNFLKDYEPDLYRE 81 (337)
T ss_pred ecCCCC--CCCHHHHHHHhcCCChHH
Confidence 444433 456777777777777754
No 185
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=26.01 E-value=20 Score=22.55 Aligned_cols=9 Identities=33% Similarity=1.187 Sum_probs=4.5
Q ss_pred CCCCCCCCC
Q 030491 49 CPYCYEDFD 57 (176)
Q Consensus 49 CPFC~e~fD 57 (176)
||-|+..+.
T Consensus 2 CP~C~~~l~ 10 (41)
T PF13453_consen 2 CPRCGTELE 10 (41)
T ss_pred cCCCCcccc
Confidence 555554444
No 186
>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=25.63 E-value=17 Score=28.58 Aligned_cols=22 Identities=27% Similarity=0.671 Sum_probs=15.5
Q ss_pred CCcccCCCCCC-CCCHHHHHhhh
Q 030491 44 RPDFPCPYCYE-DFDIASLCSHL 65 (176)
Q Consensus 44 r~~F~CPFC~e-~fDv~~L~~H~ 65 (176)
-..|.||||+. .-.+..+....
T Consensus 4 ~~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 4 WSDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred EecCcCccHHHHHHHHHHHHHhC
Confidence 35799999998 55666666554
No 187
>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=25.56 E-value=46 Score=23.33 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=7.0
Q ss_pred cCCCCCCCCC
Q 030491 48 PCPYCYEDFD 57 (176)
Q Consensus 48 ~CPFC~e~fD 57 (176)
-||+||+.++
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 4888888544
No 188
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.49 E-value=42 Score=31.08 Aligned_cols=23 Identities=30% Similarity=0.750 Sum_probs=19.0
Q ss_pred CCCCcccCCCCCCCCCHHHHHhh
Q 030491 42 DVRPDFPCPYCYEDFDIASLCSH 64 (176)
Q Consensus 42 d~r~~F~CPFC~e~fDv~~L~~H 64 (176)
-+...|+||.|+..|-..+|..|
T Consensus 16 q~~~~fpc~ic~r~f~~~~L~kh 38 (351)
T KOG3940|consen 16 QMQMRFPCRICQREFRRRELMKH 38 (351)
T ss_pred cccccccccccccchhhhhhhcc
Confidence 34569999999998888888776
No 189
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=25.28 E-value=39 Score=30.10 Aligned_cols=43 Identities=16% Similarity=0.404 Sum_probs=27.2
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccchhhHHHHhhhhccc
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHGH 99 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~s~d~l~HL~~rH~~ 99 (176)
..||.|+.. + +..+ ++....||--|-..+..+++.+-.--+.|
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 369999884 1 1112 23567999999998877766544333333
No 190
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=25.02 E-value=42 Score=34.60 Aligned_cols=53 Identities=25% Similarity=0.476 Sum_probs=35.9
Q ss_pred CCCcccCCCCCCCCCHH-HHHhhhhhhccCCCcceecCcccccc--hhhHHHHhhhhc
Q 030491 43 VRPDFPCPYCYEDFDIA-SLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQH 97 (176)
Q Consensus 43 ~r~~F~CPFC~e~fDv~-~L~~H~~eeH~~e~k~vVCPICaa~~--s~d~l~HL~~rH 97 (176)
.-..|.|+-||+-|-.. -|-+|+... ..-|.--||-|-.+. +..+-.||...-
T Consensus 278 ~lRKFKCtECgKAFKfKHHLKEHlRIH--SGEKPfeCpnCkKRFSHSGSySSHmSSKK 333 (1007)
T KOG3623|consen 278 LLRKFKCTECGKAFKFKHHLKEHLRIH--SGEKPFECPNCKKRFSHSGSYSSHMSSKK 333 (1007)
T ss_pred hhccccccccchhhhhHHHHHhhheee--cCCCCcCCcccccccccCCcccccccccc
Confidence 45689999999966543 344444432 356788999999986 456667775443
No 191
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=24.99 E-value=40 Score=31.65 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=9.0
Q ss_pred CCCcccCCCCCC
Q 030491 43 VRPDFPCPYCYE 54 (176)
Q Consensus 43 ~r~~F~CPFC~e 54 (176)
....|.|+.||-
T Consensus 422 ~~~~~~c~~c~~ 433 (479)
T PRK05452 422 LGPRMQCSVCQW 433 (479)
T ss_pred CCCeEEECCCCe
Confidence 356799999965
No 192
>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=24.94 E-value=20 Score=32.29 Aligned_cols=19 Identities=32% Similarity=0.667 Sum_probs=12.7
Q ss_pred hccCCCcceecCcccccch
Q 030491 68 EHSCESKVTVCPICSVKVA 86 (176)
Q Consensus 68 eH~~e~k~vVCPICaa~~s 86 (176)
....+++.-|||||...|+
T Consensus 25 ~~~~~pNt~v~~~~lg~PG 43 (289)
T PF02934_consen 25 EFGAEPNTNVCPVCLGLPG 43 (289)
T ss_dssp STTSCTTSSB-TTTTT-TT
T ss_pred CCCCCCccccCceeccCCC
Confidence 3334688899999999974
No 193
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.80 E-value=32 Score=28.14 Aligned_cols=32 Identities=22% Similarity=0.544 Sum_probs=18.0
Q ss_pred cCCCCCCCCCHHHHHhhhhhhccCCCcc-----eecCcccccc
Q 030491 48 PCPYCYEDFDIASLCSHLEDEHSCESKV-----TVCPICSVKV 85 (176)
Q Consensus 48 ~CPFC~e~fDv~~L~~H~~eeH~~e~k~-----vVCPICaa~~ 85 (176)
.|||||.... |+.+.-.....+ --||-|...-
T Consensus 2 ~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCcc
Confidence 6999997431 222222222322 4599998763
No 194
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=24.71 E-value=41 Score=33.60 Aligned_cols=55 Identities=25% Similarity=0.561 Sum_probs=34.2
Q ss_pred CCCCCCCcccCCCCCC-CCC-HHHHHhh-----hhhh---ccCCCcceecCcccccchhhHHHHh
Q 030491 39 VEDDVRPDFPCPYCYE-DFD-IASLCSH-----LEDE---HSCESKVTVCPICSVKVARDMLSHI 93 (176)
Q Consensus 39 ~ddd~r~~F~CPFC~e-~fD-v~~L~~H-----~~ee---H~~e~k~vVCPICaa~~s~d~l~HL 93 (176)
..+|....--|-+|.+ -=| +.+-|.| |..+ -..+..+|-||+|.-..+.|+-.|-
T Consensus 529 ~~~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 529 LPDENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred CCccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 3445667788999977 222 3333333 3322 2347778999999988776655543
No 195
>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=24.66 E-value=60 Score=24.01 Aligned_cols=30 Identities=30% Similarity=0.523 Sum_probs=24.0
Q ss_pred CCCcceecCcccccc-hhhHHHHhhhhccch
Q 030491 71 CESKVTVCPICSVKV-ARDMLSHITLQHGHL 100 (176)
Q Consensus 71 ~e~k~vVCPICaa~~-s~d~l~HL~~rH~~~ 100 (176)
.+.+.+||-.|-..+ ..++.+||..+|...
T Consensus 7 ~~~~vlIC~~C~~av~~~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 7 PEYRVLICRQCQYAVQPSEVESHLRKRHHIL 37 (109)
T ss_pred CcCCEEEeCCCCcccCchHHHHHHHHhcccc
Confidence 466789999997654 589999999888654
No 196
>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=24.32 E-value=25 Score=25.70 Aligned_cols=9 Identities=44% Similarity=1.375 Sum_probs=8.0
Q ss_pred cccCCCCCC
Q 030491 46 DFPCPYCYE 54 (176)
Q Consensus 46 ~F~CPFC~e 54 (176)
.|.||||..
T Consensus 14 D~~Cp~C~~ 22 (154)
T cd03023 14 DYNCGYCKK 22 (154)
T ss_pred CCCChhHHH
Confidence 689999987
No 197
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.30 E-value=41 Score=31.53 Aligned_cols=18 Identities=28% Similarity=0.850 Sum_probs=0.0
Q ss_pred eecCcccccc-hhhHHHHh
Q 030491 76 TVCPICSVKV-ARDMLSHI 93 (176)
Q Consensus 76 vVCPICaa~~-s~d~l~HL 93 (176)
|.||||..++ ...+-.||
T Consensus 182 v~CPiC~~~~~~~~i~~Hl 200 (397)
T TIGR00599 182 VQCPICQQRMPEKAVERHL 200 (397)
T ss_pred ccCCCcccccCHHHHHHHH
No 198
>PF04551 GcpE: GcpE protein; InterPro: IPR004588 This protein previously of unknown biochemical function is essential in Escherichia coli. It has now been characterised as 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, which converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4CPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate in the sixth step of nonmevalonate terpenoid biosynthesis. The family is largely restricted to bacteria, where it is widely but not universally distributed. No homology can be detected between this family and other proteins.; GO: 0046429 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase activity, 0016114 terpenoid biosynthetic process, 0055114 oxidation-reduction process; PDB: 2Y0F_C 3NOY_A.
Probab=23.94 E-value=40 Score=31.37 Aligned_cols=81 Identities=22% Similarity=0.354 Sum_probs=38.7
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccCCC--cceecCccccc-chh----hHHHH-hhhhccchhhhhhcccccccCCCC
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSCES--KVTVCPICSVK-VAR----DMLSH-ITLQHGHLFKLQRRRRLRRVAIPS 116 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~e~--k~vVCPICaa~-~s~----d~l~H-L~~rH~~~~k~~r~rr~rr~~~p~ 116 (176)
.-.||=||. .||+.++..-+++.=..=. -.+-==-|..+ |+. ||--= -...-+..| +++..++|. +|.
T Consensus 268 ~ISCPtCGRt~~Dl~~~~~~ie~~l~~l~~~lkIAVMGCiVNGPGEa~~AD~GiaGgg~g~~~lf--~~g~~v~k~-~~e 344 (359)
T PF04551_consen 268 IISCPTCGRTEFDLQELVAEIEERLKHLKKGLKIAVMGCIVNGPGEAKDADIGIAGGGKGKGILF--KKGEVVKKV-IPE 344 (359)
T ss_dssp EEE----TT--SHHHHHHHHHHHHCCCHHCG-EEEEESSTCCCHHHCTTSSEEEE-E-TTCEEEE--CTTEEEEEE--CS
T ss_pred eeeCCCCCCccchHHHHHHHHHHHHhcCCCCceEEEEeeeecCCchhhhCceeeecCCCCeEEEE--ECCEEEEec-CCH
Confidence 689999999 9999999998887633211 11111125554 321 22100 000113455 245556665 467
Q ss_pred chhHhhhhhhhhh
Q 030491 117 SQALSLLGRDLRE 129 (176)
Q Consensus 117 ~s~ls~l~kelre 129 (176)
......|.+++++
T Consensus 345 e~~vd~L~~~I~~ 357 (359)
T PF04551_consen 345 EEIVDELIELIEE 357 (359)
T ss_dssp TCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh
Confidence 6777767666543
No 199
>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=23.30 E-value=13 Score=30.14 Aligned_cols=13 Identities=31% Similarity=0.518 Sum_probs=10.0
Q ss_pred CCCcccCCCCCCC
Q 030491 43 VRPDFPCPYCYED 55 (176)
Q Consensus 43 ~r~~F~CPFC~e~ 55 (176)
.-..|.||||+-+
T Consensus 5 ~~~D~vcPwcylg 17 (209)
T cd03021 5 LYYDVVSPYSYLA 17 (209)
T ss_pred EEEeCCChHHHHH
Confidence 3457999999873
No 200
>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=23.29 E-value=5 Score=29.26 Aligned_cols=38 Identities=24% Similarity=0.492 Sum_probs=14.9
Q ss_pred cCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 48 ~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
.||-|...++..+-.-||..=...=...+.||-|-...
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHH
Confidence 45555555544442112211111123468899998764
No 201
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=23.26 E-value=51 Score=21.44 Aligned_cols=23 Identities=22% Similarity=0.469 Sum_probs=13.4
Q ss_pred cCCCCCCCCCHHHHHhhhhhhccCCCcceecCccc
Q 030491 48 PCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICS 82 (176)
Q Consensus 48 ~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICa 82 (176)
.||-|+--+-. .....++||+|.
T Consensus 19 ~Cp~C~~PL~~------------~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPLMR------------DKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCeeEE------------ecCCCEECCCCC
Confidence 68888653321 123457888883
No 202
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.22 E-value=26 Score=27.30 Aligned_cols=11 Identities=27% Similarity=0.748 Sum_probs=6.8
Q ss_pred ccCCCCCC-CCC
Q 030491 47 FPCPYCYE-DFD 57 (176)
Q Consensus 47 F~CPFC~e-~fD 57 (176)
|.||.||- +++
T Consensus 93 ~~CP~Cgs~~~~ 104 (124)
T PRK00762 93 IECPVCGNKRAH 104 (124)
T ss_pred CcCcCCCCCCCE
Confidence 56777764 443
No 203
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=22.94 E-value=46 Score=28.78 Aligned_cols=27 Identities=22% Similarity=0.525 Sum_probs=17.8
Q ss_pred ccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
=.||+||..+... .+....+||-|...
T Consensus 100 ~fC~~CG~~~~~~-----------~~~~~~~C~~c~~~ 126 (256)
T PRK00241 100 RFCGYCGHPMHPS-----------KTEWAMLCPHCRER 126 (256)
T ss_pred ccccccCCCCeec-----------CCceeEECCCCCCE
Confidence 3699999965432 23445678888765
No 204
>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=22.74 E-value=37 Score=28.24 Aligned_cols=12 Identities=50% Similarity=1.281 Sum_probs=2.7
Q ss_pred CCCCcccCCCCC
Q 030491 42 DVRPDFPCPYCY 53 (176)
Q Consensus 42 d~r~~F~CPFC~ 53 (176)
|.+..|.||||.
T Consensus 150 ~~~~~~~Cp~C~ 161 (175)
T PF05280_consen 150 DPRHSFVCPFCQ 161 (175)
T ss_dssp --SS----TT--
T ss_pred CCCcCcCCCCCC
Confidence 445667777774
No 205
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.58 E-value=28 Score=35.01 Aligned_cols=41 Identities=24% Similarity=0.430 Sum_probs=26.5
Q ss_pred CCCCcccCCCCCCCC----CHHHHHhhhhhhccCCCcceecCccccc
Q 030491 42 DVRPDFPCPYCYEDF----DIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 42 d~r~~F~CPFC~e~f----Dv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
+....+.||.|+..+ +...|.||-=..+ +..+-.||=|-..
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 345679999998743 2345555433322 5677899999876
No 206
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.56 E-value=37 Score=27.46 Aligned_cols=26 Identities=23% Similarity=0.623 Sum_probs=18.3
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
...||-||--+-. -...|+||||-.+
T Consensus 28 ~~hCp~Cg~PLF~-------------KdG~v~CPvC~~~ 53 (131)
T COG1645 28 AKHCPKCGTPLFR-------------KDGEVFCPVCGYR 53 (131)
T ss_pred HhhCcccCCccee-------------eCCeEECCCCCce
Confidence 4789999974311 2457999999854
No 207
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=22.37 E-value=42 Score=26.33 Aligned_cols=17 Identities=29% Similarity=0.763 Sum_probs=13.4
Q ss_pred CcccCCCCCC--CCCHHHH
Q 030491 45 PDFPCPYCYE--DFDIASL 61 (176)
Q Consensus 45 ~~F~CPFC~e--~fDv~~L 61 (176)
..|.||.|+. +||..|=
T Consensus 19 ~~w~C~~C~q~N~f~e~Gd 37 (131)
T PF09779_consen 19 SNWTCPHCEQYNGFDEDGD 37 (131)
T ss_pred CeeECCCCCCccCccccCC
Confidence 3599999987 8887663
No 208
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.27 E-value=43 Score=26.54 Aligned_cols=14 Identities=43% Similarity=0.866 Sum_probs=11.4
Q ss_pred cccCCCCCCCCCHH
Q 030491 46 DFPCPYCYEDFDIA 59 (176)
Q Consensus 46 ~F~CPFC~e~fDv~ 59 (176)
...||-||+.|+-.
T Consensus 49 ~t~CP~Cg~~~e~~ 62 (115)
T COG1885 49 STSCPKCGEPFESA 62 (115)
T ss_pred cccCCCCCCcccee
Confidence 57899999988754
No 209
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=22.19 E-value=37 Score=27.92 Aligned_cols=31 Identities=23% Similarity=0.608 Sum_probs=18.2
Q ss_pred cCCCCCC-CCCHHHHHhhhhhhccCCCcce-----ecCcccccc
Q 030491 48 PCPYCYE-DFDIASLCSHLEDEHSCESKVT-----VCPICSVKV 85 (176)
Q Consensus 48 ~CPFC~e-~fDv~~L~~H~~eeH~~e~k~v-----VCPICaa~~ 85 (176)
.||||+. +--+ .+.-..+..+. -|+.|..+-
T Consensus 2 ~CP~C~~~dtkV-------iDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 2 HCPFCQHHNTRV-------LDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCEe-------eeccccCCCCeeeecccCCccCCcc
Confidence 5999987 4332 22333333333 399999873
No 210
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=22.07 E-value=38 Score=25.47 Aligned_cols=37 Identities=32% Similarity=0.535 Sum_probs=23.5
Q ss_pred cCCCCCC-CCCH---HHHHhhhhhhccC------CCcceecCccccc
Q 030491 48 PCPYCYE-DFDI---ASLCSHLEDEHSC------ESKVTVCPICSVK 84 (176)
Q Consensus 48 ~CPFC~e-~fDv---~~L~~H~~eeH~~------e~k~vVCPICaa~ 84 (176)
.||-|.. +-|- -+-|.|.--.|+. +..+..||+|...
T Consensus 34 ~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~ 80 (85)
T PF12861_consen 34 CCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQP 80 (85)
T ss_pred CCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCe
Confidence 3787766 4442 2447777666663 3456899999753
No 211
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=21.75 E-value=36 Score=21.46 Aligned_cols=11 Identities=18% Similarity=0.682 Sum_probs=7.4
Q ss_pred CCcccCCCCCC
Q 030491 44 RPDFPCPYCYE 54 (176)
Q Consensus 44 r~~F~CPFC~e 54 (176)
...+.||||+.
T Consensus 22 ~~~w~C~~C~~ 32 (40)
T PF04810_consen 22 GKTWICNFCGT 32 (40)
T ss_dssp TTEEEETTT--
T ss_pred CCEEECcCCCC
Confidence 35899999986
No 212
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=21.65 E-value=51 Score=29.77 Aligned_cols=30 Identities=27% Similarity=0.596 Sum_probs=20.8
Q ss_pred cCCCCCC--CCCCCCCcccCCCCCC--CCCHHHH
Q 030491 32 LSIDDFE--VEDDVRPDFPCPYCYE--DFDIASL 61 (176)
Q Consensus 32 ~g~d~~~--~ddd~r~~F~CPFC~e--~fDv~~L 61 (176)
+|-||++ .|+|-..+-.|+||+. .||..++
T Consensus 250 lg~eEi~~m~eedg~iev~C~FC~~~Y~f~~~ei 283 (286)
T COG1281 250 LGKEELEDMLEEDGGIEVTCEFCGTKYLFDEEEI 283 (286)
T ss_pred cCHHHHHHHHhcCCCeEEEeeccCCEEecCHHHH
Confidence 4545543 2445677899999999 8887765
No 213
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=21.56 E-value=75 Score=25.63 Aligned_cols=40 Identities=15% Similarity=0.277 Sum_probs=28.4
Q ss_pred cccCCCCCC--CCCH---HHHHhhhhhhccCCCc------ceecCcccccc
Q 030491 46 DFPCPYCYE--DFDI---ASLCSHLEDEHSCESK------VTVCPICSVKV 85 (176)
Q Consensus 46 ~F~CPFC~e--~fDv---~~L~~H~~eeH~~e~k------~vVCPICaa~~ 85 (176)
-|.|=-||+ +|+. ..+...+...+.+... .++||-|....
T Consensus 100 H~iC~~CGki~~i~~~~l~~~~~~~~~~~gf~i~~~~l~~~GiC~~C~~~~ 150 (169)
T PRK11639 100 MFICDRCGAVKEECAEGVEDIMHTLAAKMGFALRHNVIEAHGLCAACVEVE 150 (169)
T ss_pred eEEeCCCCCEEEecccHHHHHHHHHHHHcCCEEeccEEEEEEEChhhcCcc
Confidence 499999999 7763 3456667777766432 37899997764
No 214
>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=21.55 E-value=46 Score=23.22 Aligned_cols=9 Identities=44% Similarity=1.110 Sum_probs=8.0
Q ss_pred cccCCCCCC
Q 030491 46 DFPCPYCYE 54 (176)
Q Consensus 46 ~F~CPFC~e 54 (176)
..+||||+.
T Consensus 35 ~~pC~fCg~ 43 (57)
T PF06221_consen 35 LGPCPFCGT 43 (57)
T ss_pred cCcCCCCCC
Confidence 579999998
No 215
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.36 E-value=54 Score=29.61 Aligned_cols=29 Identities=28% Similarity=0.460 Sum_probs=21.5
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
-..||-|++-+....|-. +.-|||-|...
T Consensus 38 w~kc~~C~~~~~~~~l~~----------~~~vcp~c~~h 66 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKS----------KMNICEQCGYH 66 (296)
T ss_pred eeECCCccchhhHHHHHH----------cCCCCCCCCCC
Confidence 467999999777666543 34699999775
No 216
>PF14279 HNH_5: HNH endonuclease
Probab=21.18 E-value=34 Score=24.43 Aligned_cols=40 Identities=23% Similarity=0.477 Sum_probs=22.2
Q ss_pred CCCCCCCCCHHHH-HhhhhhhccC---CCcceecCcccccchhhH
Q 030491 49 CPYCYEDFDIASL-CSHLEDEHSC---ESKVTVCPICSVKVARDM 89 (176)
Q Consensus 49 CPFC~e~fDv~~L-~~H~~eeH~~---e~k~vVCPICaa~~s~d~ 89 (176)
|.||.++++.... .+|+--+=-. ..+. ||--|-...+.+.
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~v 44 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN-VCDKCNNKFGSKV 44 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc-hhHHHhHHHhHHH
Confidence 8999986655432 3343333211 2233 8888877765433
No 217
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=21.11 E-value=38 Score=26.69 Aligned_cols=36 Identities=25% Similarity=0.646 Sum_probs=20.1
Q ss_pred CCcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 44 r~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
...|.||||.-+= ..-+-++..|. ....-|-||..-
T Consensus 21 dt~FnClfcnHek---~v~~~~Dk~~~--iG~~sC~iC~es 56 (109)
T KOG3214|consen 21 DTQFNCLFCNHEK---SVSCTLDKKHN--IGKASCRICEES 56 (109)
T ss_pred heeeccCcccccc---ceeeeehhhcC--cceeeeeehhhh
Confidence 3479999996521 11111222322 335679999764
No 218
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=21.07 E-value=41 Score=21.82 Aligned_cols=7 Identities=57% Similarity=1.554 Sum_probs=3.2
Q ss_pred cCCCCCC
Q 030491 48 PCPYCYE 54 (176)
Q Consensus 48 ~CPFC~e 54 (176)
+||.|+-
T Consensus 5 pCP~CGG 11 (40)
T PF08273_consen 5 PCPICGG 11 (40)
T ss_dssp --TTTT-
T ss_pred CCCCCcC
Confidence 6888854
No 219
>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=21.04 E-value=75 Score=23.50 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=23.4
Q ss_pred CcccC----CCCCC-CCCHHHHHhhhhhhcc
Q 030491 45 PDFPC----PYCYE-DFDIASLCSHLEDEHS 70 (176)
Q Consensus 45 ~~F~C----PFC~e-~fDv~~L~~H~~eeH~ 70 (176)
.-|.| +.|+- --+...+..|+..+|.
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 46999 99988 9999999999999984
No 220
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=20.98 E-value=17 Score=28.08 Aligned_cols=20 Identities=30% Similarity=0.653 Sum_probs=12.6
Q ss_pred CCcccCCCCCCCCC-HHHHHh
Q 030491 44 RPDFPCPYCYEDFD-IASLCS 63 (176)
Q Consensus 44 r~~F~CPFC~e~fD-v~~L~~ 63 (176)
-..|.||||+-+.. +..+..
T Consensus 4 ~~D~~cP~cy~~~~~l~~~~~ 24 (192)
T cd03022 4 YFDFSSPYSYLAHERLPALAA 24 (192)
T ss_pred EEeCCChHHHHHHHHHHHHHH
Confidence 35789999987332 344444
No 221
>PRK05978 hypothetical protein; Provisional
Probab=20.93 E-value=27 Score=28.58 Aligned_cols=28 Identities=25% Similarity=0.443 Sum_probs=17.9
Q ss_pred cccCCCCCC-CCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e-~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
.-.||-||+ .+=. .+-.-+-.||+|-..
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 333345568888765
No 222
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.81 E-value=41 Score=19.18 Aligned_cols=6 Identities=50% Similarity=1.398 Sum_probs=2.7
Q ss_pred CCCCCC
Q 030491 49 CPYCYE 54 (176)
Q Consensus 49 CPFC~e 54 (176)
||.||.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 444444
No 223
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=20.46 E-value=45 Score=28.58 Aligned_cols=19 Identities=32% Similarity=0.695 Sum_probs=15.8
Q ss_pred ecCcccccc--hhhHHHHhhh
Q 030491 77 VCPICSVKV--ARDMLSHITL 95 (176)
Q Consensus 77 VCPICaa~~--s~d~l~HL~~ 95 (176)
.|-||-..+ +.||+.||+.
T Consensus 77 yCdVCdcvvKDSinflDHiNg 97 (193)
T KOG4727|consen 77 YCDVCDCVVKDSINFLDHING 97 (193)
T ss_pred eeeecceeehhhHHHHHHhcc
Confidence 499998776 7899999974
No 224
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.21 E-value=30 Score=31.61 Aligned_cols=17 Identities=41% Similarity=0.962 Sum_probs=13.9
Q ss_pred ccCCCCCCCCCHHHHHh
Q 030491 47 FPCPYCYEDFDIASLCS 63 (176)
Q Consensus 47 F~CPFC~e~fDv~~L~~ 63 (176)
=+||||-|.+|.+.+-+
T Consensus 271 qtCPYCKekVdl~rmfs 287 (328)
T KOG1734|consen 271 QTCPYCKEKVDLKRMFS 287 (328)
T ss_pred CCCchHHHHhhHhhhcc
Confidence 47999999988887654
No 225
>TIGR00612 ispG_gcpE 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase. Chlamydial members of the family have a long insert. The family is largely restricted to Bacteria, where it is widely but not universally distributed. No homology can be detected between the GcpE family and other proteins.
Probab=20.14 E-value=83 Score=29.25 Aligned_cols=27 Identities=19% Similarity=0.477 Sum_probs=23.4
Q ss_pred CcccCCCCCC-CCCHHHHHhhhhhhccC
Q 030491 45 PDFPCPYCYE-DFDIASLCSHLEDEHSC 71 (176)
Q Consensus 45 ~~F~CPFC~e-~fDv~~L~~H~~eeH~~ 71 (176)
..-.||-||. ++|+..+..-+++.-..
T Consensus 258 ~iiSCPtCGR~~~dl~~~~~~ve~~l~~ 285 (346)
T TIGR00612 258 EIVACPSCGRTGFDVEKVVRRVQEALFH 285 (346)
T ss_pred eEEECCCCCCcCCCHHHHHHHHHHHHhc
Confidence 4689999999 99999999999887554
No 226
>COG1773 Rubredoxin [Energy production and conversion]
Probab=20.12 E-value=54 Score=22.88 Aligned_cols=14 Identities=36% Similarity=0.859 Sum_probs=11.0
Q ss_pred CCCCCcccCCCCCC
Q 030491 41 DDVRPDFPCPYCYE 54 (176)
Q Consensus 41 dd~r~~F~CPFC~e 54 (176)
+|+...+.||-|+.
T Consensus 31 edlPd~w~CP~Cg~ 44 (55)
T COG1773 31 EDLPDDWVCPECGV 44 (55)
T ss_pred hhCCCccCCCCCCC
Confidence 35567899999985
No 227
>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=20.12 E-value=64 Score=28.75 Aligned_cols=29 Identities=28% Similarity=0.552 Sum_probs=21.2
Q ss_pred cccCCCCCCCCCHHHHHhhhhhhccCCCcceecCccccc
Q 030491 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (176)
Q Consensus 46 ~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~ 84 (176)
-..||-|++-+-..+|.. +..|||-|...
T Consensus 26 ~~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELER----------NLEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHh----------hCCCCCCCCCc
Confidence 467999999776666543 34699999775
No 228
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=20.08 E-value=66 Score=26.62 Aligned_cols=36 Identities=19% Similarity=0.511 Sum_probs=24.4
Q ss_pred CcccCCCCCCCCCHHHHHhhhhhhccCCCcceecCcccccc
Q 030491 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (176)
Q Consensus 45 ~~F~CPFC~e~fDv~~L~~H~~eeH~~e~k~vVCPICaa~~ 85 (176)
....|.-|++.+....+..+.. +...-.||.|....
T Consensus 108 ~~~~C~~C~~~~~~~~~~~~~~-----~~~~p~C~~Cg~~l 143 (218)
T cd01407 108 FRVRCTKCGKEYPRDELQADID-----REEVPRCPKCGGLL 143 (218)
T ss_pred CcceeCCCcCCCcHHHHhHhhc-----cCCCCcCCCCCCcc
Confidence 4578999999887776653322 23345799997664
Done!