Query 027446
Match_columns 223
No_of_seqs 151 out of 185
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 10:03:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027446.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027446hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14571 Di19_C: Stress-induce 100.0 3.8E-35 8.2E-40 230.5 7.3 103 115-218 1-105 (105)
2 PF05605 zf-Di19: Drought indu 99.8 2E-19 4.4E-24 125.0 2.4 54 43-96 1-54 (54)
3 KOG1280 Uncharacterized conser 98.5 6.1E-08 1.3E-12 90.1 4.4 108 21-135 60-182 (381)
4 COG5216 Uncharacterized conser 94.1 0.014 3E-07 42.3 0.0 37 39-84 17-55 (67)
5 KOG2923 Uncharacterized conser 93.5 0.031 6.8E-07 40.9 0.9 45 31-84 8-55 (67)
6 PF13894 zf-C2H2_4: C2H2-type 93.4 0.027 6E-07 31.2 0.4 23 45-67 1-24 (24)
7 COG5236 Uncharacterized conser 92.0 0.13 2.8E-06 49.0 3.1 33 44-82 220-253 (493)
8 PHA00732 hypothetical protein 91.1 0.17 3.7E-06 38.0 2.3 42 45-91 2-44 (79)
9 PF12756 zf-C2H2_2: C2H2 type 91.0 0.11 2.4E-06 38.0 1.2 47 46-92 1-71 (100)
10 smart00531 TFIIE Transcription 90.8 0.2 4.2E-06 41.2 2.7 41 39-84 94-134 (147)
11 TIGR02098 MJ0042_CXXC MJ0042 f 90.4 0.19 4.2E-06 31.9 1.8 34 44-83 2-35 (38)
12 smart00834 CxxC_CXXC_SSSS Puta 90.4 0.18 4E-06 32.1 1.7 33 43-83 4-36 (41)
13 PF13913 zf-C2HC_2: zinc-finge 89.9 0.14 3E-06 30.4 0.8 21 44-64 2-22 (25)
14 PF00096 zf-C2H2: Zinc finger, 89.8 0.083 1.8E-06 29.7 -0.3 21 45-65 1-22 (23)
15 PF09237 GAGA: GAGA factor; I 89.5 0.21 4.6E-06 35.2 1.5 27 71-97 22-50 (54)
16 PF08271 TF_Zn_Ribbon: TFIIB z 89.5 0.15 3.3E-06 33.5 0.8 36 45-90 1-36 (43)
17 PLN03086 PRLI-interacting fact 89.3 0.25 5.5E-06 49.3 2.5 45 43-92 452-497 (567)
18 TIGR01206 lysW lysine biosynth 89.2 0.2 4.4E-06 35.3 1.3 31 44-83 2-32 (54)
19 PRK09710 lar restriction allev 89.1 0.16 3.5E-06 37.1 0.7 31 45-84 7-38 (64)
20 PF13909 zf-H2C2_5: C2H2-type 87.6 0.15 3.3E-06 29.1 -0.1 24 45-68 1-24 (24)
21 KOG2462 C2H2-type Zn-finger pr 87.1 0.41 8.9E-06 43.9 2.2 37 42-82 159-196 (279)
22 PF14354 Lar_restr_allev: Rest 86.3 0.29 6.4E-06 34.0 0.7 31 44-81 3-37 (61)
23 TIGR02605 CxxC_CxxC_SSSS putat 86.1 0.49 1.1E-05 31.9 1.7 32 43-82 4-35 (52)
24 PHA00733 hypothetical protein 85.7 0.73 1.6E-05 37.3 2.8 50 43-96 72-124 (128)
25 PF08274 PhnA_Zn_Ribbon: PhnA 85.6 0.32 7E-06 30.4 0.5 24 46-81 4-27 (30)
26 PHA02768 hypothetical protein; 85.4 0.43 9.3E-06 33.9 1.1 34 44-81 5-39 (55)
27 KOG2462 C2H2-type Zn-finger pr 84.8 0.81 1.8E-05 42.0 2.9 84 44-133 187-273 (279)
28 PF09986 DUF2225: Uncharacteri 83.7 0.51 1.1E-05 41.2 1.1 42 44-85 5-60 (214)
29 PRK14892 putative transcriptio 83.4 0.66 1.4E-05 36.5 1.5 36 41-85 18-54 (99)
30 PF09723 Zn-ribbon_8: Zinc rib 83.0 0.67 1.4E-05 30.6 1.2 31 43-81 4-34 (42)
31 KOG1842 FYVE finger-containing 82.7 0.52 1.1E-05 46.0 0.9 35 39-73 10-45 (505)
32 PF07191 zinc-ribbons_6: zinc- 82.6 0.24 5.3E-06 36.8 -1.1 55 45-103 2-63 (70)
33 cd00350 rubredoxin_like Rubred 82.5 0.92 2E-05 28.4 1.6 25 45-82 2-26 (33)
34 PLN03086 PRLI-interacting fact 81.4 1 2.2E-05 45.2 2.3 39 43-84 477-515 (567)
35 PRK00398 rpoP DNA-directed RNA 81.1 0.94 2E-05 30.1 1.4 29 44-83 3-31 (46)
36 PF14206 Cys_rich_CPCC: Cystei 78.9 1.1 2.3E-05 33.9 1.2 25 45-80 2-27 (78)
37 cd00729 rubredoxin_SM Rubredox 78.4 1.6 3.4E-05 27.7 1.7 26 44-82 2-27 (34)
38 COG4888 Uncharacterized Zn rib 77.8 0.9 1.9E-05 36.1 0.5 37 42-83 20-56 (104)
39 PF12773 DZR: Double zinc ribb 77.1 1.8 3.9E-05 28.8 1.8 27 46-84 14-40 (50)
40 PRK06266 transcription initiat 77.1 2 4.3E-05 36.7 2.5 36 39-84 112-147 (178)
41 PF14255 Cys_rich_CPXG: Cystei 77.0 0.92 2E-05 31.7 0.4 35 45-84 1-35 (52)
42 smart00504 Ubox Modified RING 76.8 1.5 3.4E-05 29.9 1.5 25 54-85 23-47 (63)
43 TIGR00373 conserved hypothetic 76.0 2.1 4.7E-05 35.7 2.4 36 39-84 104-139 (158)
44 COG2888 Predicted Zn-ribbon RN 75.3 2.6 5.7E-05 30.5 2.3 34 39-80 22-57 (61)
45 PRK14890 putative Zn-ribbon RN 75.0 2.2 4.9E-05 30.7 1.9 35 40-81 21-56 (59)
46 PF02176 zf-TRAF: TRAF-type zi 74.7 1.7 3.8E-05 29.6 1.3 45 44-90 9-60 (60)
47 PF04780 DUF629: Protein of un 74.3 1.4 3.1E-05 43.2 1.0 42 41-82 54-99 (466)
48 smart00734 ZnF_Rad18 Rad18-lik 73.8 1.5 3.2E-05 26.3 0.6 9 75-83 3-11 (26)
49 PF13912 zf-C2H2_6: C2H2-type 73.1 1.8 3.8E-05 25.1 0.9 23 45-67 2-25 (27)
50 PF14353 CpXC: CpXC protein 72.5 1.5 3.3E-05 34.7 0.6 38 45-83 2-48 (128)
51 PF03145 Sina: Seven in absent 72.0 2.1 4.6E-05 36.3 1.5 54 43-99 13-75 (198)
52 PF11672 DUF3268: Protein of u 72.0 2.4 5.1E-05 33.6 1.6 38 45-85 3-43 (102)
53 PLN03208 E3 ubiquitin-protein 71.6 2.2 4.8E-05 37.3 1.5 49 40-88 14-83 (193)
54 PF12756 zf-C2H2_2: C2H2 type 70.9 1.8 3.8E-05 31.5 0.6 24 44-67 50-74 (100)
55 PF05129 Elf1: Transcription e 70.3 1.8 3.8E-05 32.7 0.5 36 41-83 19-56 (81)
56 KOG3623 Homeobox transcription 69.6 1.3 2.8E-05 45.9 -0.4 51 42-92 208-261 (1007)
57 PRK12495 hypothetical protein; 68.5 2.7 5.9E-05 37.6 1.4 31 42-85 40-70 (226)
58 PRK12496 hypothetical protein; 68.4 3 6.5E-05 35.2 1.6 27 44-83 127-153 (164)
59 PF13465 zf-H2C2_2: Zinc-finge 67.4 2.1 4.5E-05 25.2 0.3 11 44-54 14-24 (26)
60 KOG0320 Predicted E3 ubiquitin 67.1 2.4 5.2E-05 36.9 0.8 43 43-85 130-179 (187)
61 PHA00616 hypothetical protein 67.1 1.5 3.3E-05 29.8 -0.4 24 45-68 2-26 (44)
62 COG1592 Rubrerythrin [Energy p 66.6 4.5 9.8E-05 34.6 2.3 25 44-82 134-158 (166)
63 PF07754 DUF1610: Domain of un 65.7 3.9 8.4E-05 24.4 1.2 13 40-52 12-24 (24)
64 TIGR03655 anti_R_Lar restricti 65.4 2.7 5.8E-05 28.8 0.6 9 45-53 2-10 (53)
65 PTZ00255 60S ribosomal protein 65.1 2.8 6E-05 32.6 0.7 17 39-55 31-48 (90)
66 PRK00420 hypothetical protein; 64.5 3.5 7.7E-05 33.1 1.2 27 45-84 24-51 (112)
67 PF04564 U-box: U-box domain; 63.8 5.9 0.00013 28.6 2.2 38 42-85 2-51 (73)
68 PF08996 zf-DNA_Pol: DNA Polym 63.1 2.6 5.7E-05 36.0 0.2 41 42-84 16-56 (188)
69 KOG2593 Transcription initiati 62.5 3 6.5E-05 40.6 0.5 44 33-83 117-163 (436)
70 PF14446 Prok-RING_1: Prokaryo 61.9 3.5 7.5E-05 29.2 0.6 25 45-82 6-30 (54)
71 smart00659 RPOLCX RNA polymera 61.9 6.2 0.00014 26.5 1.9 28 44-83 2-29 (44)
72 TIGR00100 hypA hydrogenase nic 61.8 4 8.6E-05 32.4 1.0 30 40-82 66-95 (115)
73 smart00355 ZnF_C2H2 zinc finge 61.6 3.8 8.2E-05 22.3 0.7 20 45-64 1-21 (26)
74 PRK00464 nrdR transcriptional 61.3 6 0.00013 33.3 2.1 34 45-84 1-39 (154)
75 TIGR00280 L37a ribosomal prote 60.7 3.6 7.8E-05 32.0 0.6 15 39-53 30-44 (91)
76 PRK03976 rpl37ae 50S ribosomal 60.5 3.7 8.1E-05 31.9 0.7 17 39-55 31-48 (90)
77 PF10571 UPF0547: Uncharacteri 59.9 5.3 0.00012 24.0 1.1 9 46-54 2-10 (26)
78 PF07282 OrfB_Zn_ribbon: Putat 59.8 6.7 0.00014 27.7 1.8 41 40-91 24-64 (69)
79 PF13240 zinc_ribbon_2: zinc-r 59.5 4.2 9.1E-05 23.7 0.6 8 47-54 2-9 (23)
80 COG1645 Uncharacterized Zn-fin 59.5 4.7 0.0001 33.3 1.1 26 44-83 28-54 (131)
81 smart00507 HNHc HNH nucleases. 59.5 3.4 7.3E-05 26.2 0.2 21 45-65 11-31 (52)
82 PF14279 HNH_5: HNH endonuclea 59.2 3.7 8.1E-05 30.2 0.4 44 47-91 1-48 (71)
83 smart00661 RPOL9 RNA polymeras 59.2 5.8 0.00013 26.3 1.4 28 46-82 2-29 (52)
84 PF15616 TerY-C: TerY-C metal 58.5 4.5 9.8E-05 33.4 0.9 42 45-88 78-120 (131)
85 PF12171 zf-C2H2_jaz: Zinc-fin 58.0 6.4 0.00014 23.0 1.3 20 45-64 2-22 (27)
86 PF06957 COPI_C: Coatomer (COP 57.7 6.7 0.00014 38.1 2.0 35 42-89 378-413 (422)
87 PF13248 zf-ribbon_3: zinc-rib 57.4 6.3 0.00014 23.3 1.2 10 45-54 3-12 (26)
88 TIGR00686 phnA alkylphosphonat 57.0 5.3 0.00011 32.1 1.0 25 46-82 4-28 (109)
89 PRK03824 hypA hydrogenase nick 56.7 8.1 0.00017 31.5 2.0 43 40-82 66-116 (135)
90 PF13395 HNH_4: HNH endonuclea 56.5 5.6 0.00012 27.3 0.9 13 47-59 1-13 (54)
91 PF08209 Sgf11: Sgf11 (transcr 56.0 6.1 0.00013 25.2 1.0 20 44-63 4-23 (33)
92 PRK12380 hydrogenase nickel in 54.9 6.3 0.00014 31.2 1.1 30 40-82 66-95 (113)
93 KOG3608 Zn finger proteins [Ge 52.9 2.8 6E-05 40.3 -1.4 48 45-92 208-262 (467)
94 PF01155 HypA: Hydrogenase exp 52.2 6.9 0.00015 30.8 1.0 30 40-82 66-95 (113)
95 COG5175 MOT2 Transcriptional r 51.9 3.3 7.2E-05 39.6 -1.1 37 47-84 17-64 (480)
96 PF01780 Ribosomal_L37ae: Ribo 51.8 6.1 0.00013 30.7 0.6 17 39-55 30-47 (90)
97 smart00531 TFIIE Transcription 51.7 8.2 0.00018 31.6 1.3 13 42-54 121-133 (147)
98 PF03470 zf-XS: XS zinc finger 51.4 7.4 0.00016 26.4 0.9 10 76-85 1-10 (43)
99 COG4049 Uncharacterized protei 51.0 5.7 0.00012 28.7 0.3 26 75-100 19-46 (65)
100 COG5189 SFP1 Putative transcri 50.4 8 0.00017 36.8 1.2 41 44-84 349-409 (423)
101 PF09862 DUF2089: Protein of u 50.4 5.6 0.00012 32.0 0.2 13 47-59 1-13 (113)
102 KOG1002 Nucleotide excision re 50.1 8.6 0.00019 38.9 1.4 53 38-90 530-592 (791)
103 KOG2879 Predicted E3 ubiquitin 50.1 6.6 0.00014 36.4 0.6 43 42-84 237-287 (298)
104 COG0675 Transposase and inacti 50.0 9.4 0.0002 33.3 1.5 40 38-93 303-342 (364)
105 cd00730 rubredoxin Rubredoxin; 50.0 9.9 0.00021 26.3 1.3 14 40-53 30-43 (50)
106 COG4311 SoxD Sarcosine oxidase 49.2 7.8 0.00017 30.5 0.8 9 44-52 3-11 (97)
107 KOG2817 Predicted E3 ubiquitin 46.7 9.3 0.0002 36.9 1.0 15 42-56 372-386 (394)
108 PRK11088 rrmA 23S rRNA methylt 46.6 9.8 0.00021 33.6 1.1 30 44-75 2-34 (272)
109 PF02146 SIR2: Sir2 family; I 46.3 11 0.00024 31.3 1.3 41 43-88 104-144 (178)
110 KOG2231 Predicted E3 ubiquitin 46.1 10 0.00022 38.9 1.3 28 42-69 180-208 (669)
111 PRK03922 hypothetical protein; 46.0 9.2 0.0002 30.9 0.7 16 44-59 49-64 (113)
112 PF14616 DUF4451: Domain of un 45.6 12 0.00027 30.1 1.5 27 73-99 25-56 (124)
113 PF04475 DUF555: Protein of un 45.1 9.7 0.00021 30.2 0.7 16 44-59 47-62 (102)
114 COG5109 Uncharacterized conser 44.8 10 0.00023 35.9 1.0 12 42-53 374-385 (396)
115 PF05876 Terminase_GpA: Phage 44.7 14 0.0003 36.8 2.0 42 42-85 198-241 (557)
116 COG1198 PriA Primosomal protei 44.7 14 0.00031 38.2 2.1 41 40-82 440-484 (730)
117 PF01844 HNH: HNH endonuclease 44.6 7 0.00015 25.0 -0.1 35 47-81 1-42 (47)
118 PRK04023 DNA polymerase II lar 44.2 15 0.00032 39.6 2.1 35 181-215 778-812 (1121)
119 PF11793 FANCL_C: FANCL C-term 43.8 11 0.00023 27.4 0.8 46 40-85 16-67 (70)
120 TIGR03278 methan_mark_10 putat 43.6 14 0.0003 35.6 1.7 35 43-83 9-46 (404)
121 TIGR00570 cdk7 CDK-activating 43.6 10 0.00022 35.5 0.7 40 45-85 4-55 (309)
122 PHA02565 49 recombination endo 43.4 13 0.00028 31.7 1.3 40 45-84 21-66 (157)
123 PRK05654 acetyl-CoA carboxylas 42.6 14 0.0003 34.1 1.5 29 44-82 27-55 (292)
124 TIGR02300 FYDLN_acid conserved 42.3 13 0.00029 30.6 1.2 33 40-85 5-38 (129)
125 PRK10220 hypothetical protein; 41.8 12 0.00027 30.1 0.9 25 46-82 5-29 (111)
126 CHL00174 accD acetyl-CoA carbo 41.5 15 0.00032 34.2 1.5 29 44-82 38-66 (296)
127 PRK11595 DNA utilization prote 41.4 14 0.0003 32.2 1.2 35 46-82 7-43 (227)
128 COG1327 Predicted transcriptio 41.0 17 0.00038 30.9 1.7 33 46-84 2-39 (156)
129 KOG3214 Uncharacterized Zn rib 40.7 12 0.00025 30.0 0.6 39 41-84 20-58 (109)
130 TIGR00515 accD acetyl-CoA carb 40.6 16 0.00034 33.6 1.5 29 44-82 26-54 (285)
131 TIGR00244 transcriptional regu 40.2 20 0.00044 30.2 2.0 33 46-84 2-39 (147)
132 PF10058 DUF2296: Predicted in 39.7 16 0.00034 25.6 1.0 9 44-52 44-52 (54)
133 PF03966 Trm112p: Trm112p-like 39.3 15 0.00033 26.2 1.0 18 44-61 7-24 (68)
134 KOG0402 60S ribosomal protein 39.1 8.5 0.00018 29.8 -0.4 15 39-53 31-45 (92)
135 PF12660 zf-TFIIIC: Putative z 38.9 10 0.00022 29.4 -0.0 38 46-83 16-65 (99)
136 PF04423 Rad50_zn_hook: Rad50 38.7 13 0.00028 25.4 0.5 12 46-57 22-33 (54)
137 PF14634 zf-RING_5: zinc-RING 38.7 17 0.00037 23.6 1.1 10 71-80 34-43 (44)
138 PF14311 DUF4379: Domain of un 38.5 23 0.00049 24.2 1.7 33 39-79 23-55 (55)
139 PF13719 zinc_ribbon_5: zinc-r 38.2 30 0.00065 22.0 2.1 32 45-82 3-34 (37)
140 KOG2482 Predicted C2H2-type Zn 38.2 9.9 0.00021 36.4 -0.2 30 44-73 279-309 (423)
141 PF13717 zinc_ribbon_4: zinc-r 37.8 26 0.00056 22.3 1.8 31 45-81 3-33 (36)
142 PF10276 zf-CHCC: Zinc-finger 36.8 19 0.00041 23.9 1.0 11 44-54 29-39 (40)
143 COG1499 NMD3 NMD protein affec 36.6 20 0.00043 34.1 1.5 39 43-81 5-51 (355)
144 PF14570 zf-RING_4: RING/Ubox 36.5 11 0.00024 26.1 -0.2 33 42-81 13-45 (48)
145 cd00162 RING RING-finger (Real 35.2 8.9 0.00019 23.3 -0.7 11 72-82 34-44 (45)
146 PF12230 PRP21_like_P: Pre-mRN 34.4 13 0.00029 32.4 0.0 19 45-63 169-187 (229)
147 COG2331 Uncharacterized protei 34.4 17 0.00036 27.7 0.5 45 43-100 11-55 (82)
148 PRK05477 gatB aspartyl/glutamy 34.2 23 0.00049 35.0 1.6 16 69-84 33-48 (474)
149 PF05207 zf-CSL: CSL zinc fing 34.0 17 0.00036 25.4 0.5 44 32-84 5-51 (55)
150 PRK14714 DNA polymerase II lar 33.9 26 0.00057 38.6 2.1 35 181-215 825-859 (1337)
151 PRK03681 hypA hydrogenase nick 33.7 20 0.00043 28.4 0.9 31 40-82 66-96 (114)
152 PF09334 tRNA-synt_1g: tRNA sy 33.6 17 0.00037 34.4 0.6 41 44-84 136-177 (391)
153 COG1675 TFA1 Transcription ini 33.6 28 0.00061 30.1 1.9 32 41-84 110-143 (176)
154 smart00451 ZnF_U1 U1-like zinc 33.5 22 0.00047 21.4 0.9 20 45-64 4-24 (35)
155 PF12230 PRP21_like_P: Pre-mRN 33.3 14 0.00031 32.2 0.0 20 74-93 169-189 (229)
156 PF10609 ParA: ParA/MinD ATPas 33.2 18 0.00038 27.5 0.5 18 39-56 60-77 (81)
157 PF13824 zf-Mss51: Zinc-finger 33.0 21 0.00045 25.4 0.8 13 41-53 11-23 (55)
158 PF09706 Cas_CXXC_CXXC: CRISPR 32.9 22 0.00048 25.9 1.0 11 42-52 3-13 (69)
159 KOG2177 Predicted E3 ubiquitin 32.9 7.4 0.00016 32.2 -1.7 39 42-80 11-54 (386)
160 PRK00564 hypA hydrogenase nick 32.7 24 0.00052 28.1 1.2 31 40-82 67-97 (117)
161 PF04981 NMD3: NMD3 family ; 32.6 27 0.00059 30.7 1.7 23 193-215 145-168 (236)
162 COG0777 AccD Acetyl-CoA carbox 32.1 23 0.00051 32.9 1.2 28 45-82 29-56 (294)
163 TIGR00599 rad18 DNA repair pro 32.0 16 0.00034 35.3 0.1 46 39-84 21-71 (397)
164 smart00614 ZnF_BED BED zinc fi 31.8 21 0.00045 23.9 0.6 26 43-68 17-48 (50)
165 PF14471 DUF4428: Domain of un 31.5 11 0.00024 25.9 -0.7 30 46-83 1-30 (51)
166 PHA02929 N1R/p28-like protein; 31.5 11 0.00025 33.8 -0.9 42 43-84 173-227 (238)
167 PF11290 DUF3090: Protein of u 31.5 20 0.00044 30.9 0.7 14 45-58 155-168 (171)
168 PRK00423 tfb transcription ini 31.3 41 0.00089 30.8 2.7 40 41-90 8-47 (310)
169 PRK05452 anaerobic nitric oxid 30.9 32 0.0007 33.5 2.0 43 40-82 421-467 (479)
170 COG1405 SUA7 Transcription ini 30.9 35 0.00075 31.4 2.1 36 45-90 2-37 (285)
171 PF13453 zf-TFIIB: Transcripti 30.7 18 0.0004 23.3 0.2 27 46-81 1-27 (41)
172 PF02934 GatB_N: GatB/GatE cat 30.5 32 0.00069 31.9 1.8 26 59-84 18-43 (289)
173 PF14968 CCDC84: Coiled coil p 30.3 29 0.00062 32.9 1.5 26 39-64 53-85 (336)
174 COG4896 Uncharacterized protei 30.1 18 0.00039 26.6 0.1 50 45-98 3-54 (68)
175 PF02892 zf-BED: BED zinc fing 29.9 17 0.00037 23.4 -0.1 14 43-56 15-28 (45)
176 PF00301 Rubredoxin: Rubredoxi 29.9 20 0.00044 24.4 0.3 15 39-53 29-43 (47)
177 PRK14810 formamidopyrimidine-D 29.5 24 0.00052 31.8 0.9 29 43-80 243-271 (272)
178 PF02891 zf-MIZ: MIZ/SP-RING z 29.3 9.1 0.0002 26.1 -1.5 34 45-81 3-49 (50)
179 PF12874 zf-met: Zinc-finger o 29.1 24 0.00052 19.7 0.5 15 76-90 3-19 (25)
180 COG3058 FdhE Uncharacterized p 28.5 22 0.00047 33.2 0.4 18 72-89 184-201 (308)
181 PLN02751 glutamyl-tRNA(Gln) am 28.1 32 0.00069 34.6 1.5 22 63-84 83-104 (544)
182 PRK14714 DNA polymerase II lar 27.3 41 0.00089 37.2 2.2 37 44-84 667-703 (1337)
183 COG4391 Uncharacterized protei 26.9 30 0.00066 25.2 0.8 13 70-82 45-57 (62)
184 PF14447 Prok-RING_4: Prokaryo 26.8 36 0.00078 24.2 1.1 42 43-84 6-50 (55)
185 PF00097 zf-C3HC4: Zinc finger 26.8 8.5 0.00019 24.1 -1.9 8 72-79 34-41 (41)
186 PF04780 DUF629: Protein of un 26.6 20 0.00044 35.3 -0.2 29 72-100 56-86 (466)
187 PF09538 FYDLN_acid: Protein o 26.6 48 0.001 26.3 2.0 34 40-86 5-39 (108)
188 TIGR00595 priA primosomal prot 26.3 39 0.00084 33.2 1.7 36 44-82 222-262 (505)
189 PRK14873 primosome assembly pr 26.2 42 0.00091 34.4 1.9 39 40-82 388-431 (665)
190 PF11789 zf-Nse: Zinc-finger o 26.1 34 0.00074 24.0 1.0 15 41-55 8-22 (57)
191 PRK14559 putative protein seri 26.1 43 0.00093 34.3 2.0 39 44-85 15-53 (645)
192 KOG4628 Predicted E3 ubiquitin 26.1 29 0.00063 33.0 0.8 40 45-84 230-278 (348)
193 PF04267 SoxD: Sarcosine oxida 25.8 22 0.00048 27.2 -0.0 14 45-59 2-15 (84)
194 PF12760 Zn_Tnp_IS1595: Transp 25.6 34 0.00073 22.6 0.8 11 43-53 17-27 (46)
195 COG1656 Uncharacterized conser 25.6 41 0.00088 28.9 1.5 39 46-84 99-141 (165)
196 TIGR00133 gatB glutamyl-tRNA(G 25.2 39 0.00085 33.3 1.5 15 70-84 34-48 (478)
197 PF09889 DUF2116: Uncharacteri 24.6 36 0.00078 24.4 0.8 11 46-56 5-15 (59)
198 PRK10445 endonuclease VIII; Pr 24.5 35 0.00075 30.7 0.9 27 45-80 236-262 (263)
199 KOG3940 Uncharacterized conser 24.4 42 0.00092 31.7 1.5 25 38-62 14-38 (351)
200 COG1997 RPL43A Ribosomal prote 24.4 30 0.00066 26.9 0.5 15 39-53 30-44 (89)
201 PF03604 DNA_RNApol_7kD: DNA d 24.3 56 0.0012 20.6 1.6 11 45-55 1-11 (32)
202 PRK09678 DNA-binding transcrip 23.9 35 0.00075 25.4 0.7 9 45-53 2-10 (72)
203 PRK01103 formamidopyrimidine/5 23.8 35 0.00077 30.7 0.8 28 45-81 246-273 (274)
204 KOG4696 Uncharacterized conser 23.8 28 0.0006 33.0 0.1 22 44-65 2-23 (393)
205 PF04641 Rtf2: Rtf2 RING-finge 23.6 26 0.00057 31.3 -0.0 45 40-84 109-161 (260)
206 PF06221 zf-C2HC5: Putative zi 23.6 38 0.00081 24.2 0.8 10 44-53 35-44 (57)
207 PRK13945 formamidopyrimidine-D 23.4 37 0.0008 30.8 0.9 27 45-80 255-281 (282)
208 PF06827 zf-FPG_IleRS: Zinc fi 22.9 28 0.00061 20.9 -0.0 9 46-54 3-11 (30)
209 cd03021 DsbA_GSTK DsbA family, 22.8 17 0.00036 30.8 -1.4 13 41-53 5-17 (209)
210 KOG1074 Transcriptional repres 22.3 30 0.00065 36.7 0.1 52 45-99 354-408 (958)
211 TIGR00577 fpg formamidopyrimid 22.1 41 0.00089 30.3 0.9 26 45-79 246-271 (272)
212 KOG0978 E3 ubiquitin ligase in 22.0 24 0.00053 36.4 -0.6 47 40-86 639-691 (698)
213 PHA02776 E7 protein; Provision 22.0 25 0.00053 27.9 -0.5 38 45-82 59-100 (101)
214 PF03811 Zn_Tnp_IS1: InsA N-te 21.9 51 0.0011 21.2 1.1 9 44-52 5-13 (36)
215 PHA00626 hypothetical protein 21.9 56 0.0012 23.5 1.4 17 74-90 24-40 (59)
216 KOG0804 Cytoplasmic Zn-finger 21.8 30 0.00064 34.2 -0.1 16 43-58 174-189 (493)
217 PF06677 Auto_anti-p27: Sjogre 21.8 57 0.0012 21.6 1.3 23 46-80 19-41 (41)
218 COG0375 HybF Zn finger protein 21.7 51 0.0011 26.7 1.3 31 39-82 65-95 (115)
219 TIGR01374 soxD sarcosine oxida 21.7 39 0.00085 25.9 0.6 14 45-59 2-15 (84)
220 TIGR03847 conserved hypothetic 21.6 40 0.00086 29.3 0.7 14 45-58 157-170 (177)
221 KOG4080 Mitochondrial ribosoma 21.6 35 0.00076 29.5 0.3 28 44-87 93-120 (176)
222 cd03019 DsbA_DsbA DsbA family, 21.5 31 0.00068 27.5 0.0 11 43-53 23-33 (178)
223 cd02972 DsbA_family DsbA famil 21.5 24 0.00051 24.4 -0.6 10 44-53 6-15 (98)
224 KOG3002 Zn finger protein [Gen 21.4 38 0.00082 31.5 0.5 43 42-84 46-91 (299)
225 cd03024 DsbA_FrnE DsbA family, 21.4 23 0.0005 29.0 -0.8 20 42-61 4-24 (201)
226 PF03833 PolC_DP2: DNA polymer 21.3 32 0.00068 36.5 0.0 10 44-53 655-664 (900)
227 PRK14811 formamidopyrimidine-D 21.2 47 0.001 29.9 1.1 31 45-84 236-266 (269)
228 COG1996 RPC10 DNA-directed RNA 20.8 65 0.0014 22.4 1.5 31 42-83 4-34 (49)
229 COG1885 Uncharacterized protei 20.7 45 0.00097 26.9 0.8 16 44-59 49-64 (115)
230 PRK05580 primosome assembly pr 20.5 56 0.0012 33.3 1.6 39 42-82 388-430 (679)
231 cd03022 DsbA_HCCA_Iso DsbA fam 20.4 21 0.00046 28.9 -1.2 13 41-53 3-15 (192)
232 PRK14559 putative protein seri 20.2 70 0.0015 32.8 2.2 37 45-85 2-39 (645)
233 KOG2114 Vacuolar assembly/sort 20.2 38 0.00083 35.9 0.4 46 45-90 841-891 (933)
234 PRK00241 nudC NADH pyrophospha 20.2 51 0.0011 29.5 1.1 27 45-82 100-126 (256)
235 COG2761 FrnE Predicted dithiol 20.1 28 0.00061 31.2 -0.6 47 40-92 9-64 (225)
No 1
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=100.00 E-value=3.8e-35 Score=230.47 Aligned_cols=103 Identities=56% Similarity=0.707 Sum_probs=87.9
Q ss_pred ccccchhhhhccccccccCCC-CcccCCCCCCCCccccccccCCCCCCCCCCCCCCCCCC-ccccccCCCcccccccCCC
Q 027446 115 TFSLLRKELRDGNLQSLLGGS-SCFVSSSNTEADPLLSSFIFNTPKVDEPLSVQPLSITE-PTLVKESSNENLHERHVQQ 192 (223)
Q Consensus 115 ~~s~l~k~lre~~lq~llggs-s~~~~~sn~~pDPLLSsFi~n~~~~~~~~~~~~~~s~e-~~~~~~~s~~~~~e~~~~~ 192 (223)
|+++|+|||||||||+||||+ +++++++|++|||||||||||+|.++.++.+++..+.+ +.+.++....+.+++.++
T Consensus 1 tlsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~s~~- 79 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSEEKKSSKKSSSEQNVKSSAD- 79 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCccccccCCccccccccccccccchhcccccccC-
Confidence 689999999999999999999 56667899999999999999999999988877776655 344444455555665555
Q ss_pred CCCChHHHHHHHhHhHHHHHHHHHhh
Q 027446 193 PPLSDKDQEEKARKSEFVQGLVLSTI 218 (223)
Q Consensus 193 ~~ls~ed~eEk~~R~eFVQ~LllSTi 218 (223)
++||+||+|||+||++||||||||||
T Consensus 80 ~~lS~ee~eEk~~RseFVQ~LllSTI 105 (105)
T PF14571_consen 80 SSLSDEEQEEKAQRSEFVQGLLLSTI 105 (105)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhC
Confidence 89999999999999999999999998
No 2
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=99.76 E-value=2e-19 Score=125.00 Aligned_cols=54 Identities=37% Similarity=0.865 Sum_probs=52.0
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhhhhhhhhccc
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHITMQHG 96 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~Hi~~qH~ 96 (223)
.+|+||||+++||+.+|+.|+.++|+.+.+++|||||+.+++.||++||+.+||
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 379999999999999999999999999999999999999999999999999996
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.55 E-value=6.1e-08 Score=90.06 Aligned_cols=108 Identities=20% Similarity=0.353 Sum_probs=71.6
Q ss_pred cccccccccCCCCCCCCCCCccceeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccch---------hhhhh
Q 027446 21 QSRSDLFIGGGYDETDGDDDLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT---------DIVSH 90 (223)
Q Consensus 21 ~s~~d~~~~~~~~~~~~d~d~~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~---------d~i~H 90 (223)
..++|+|| |+|-+--+++ ..|.||||+.. |.+..+.+|+...|+.....+|||||+..+.. +...|
T Consensus 60 ~~dfeL~f--~Ge~i~~y~~--qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~~qp~~~~~~~~~~~~ 135 (381)
T KOG1280|consen 60 RVDFELYF--GGEPISHYDP--QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPEMQPIHSKETENLSVH 135 (381)
T ss_pred ccceeeEe--cCcccccccc--ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcccCchhhhhhhhhhhh
Confidence 34778888 8887764444 49999999998 99999999999999999999999999998652 44444
Q ss_pred hhhcccchhhh---cccccccCCCCCcccccchhhhhcccccc--ccCCC
Q 027446 91 ITMQHGNFFKI---QRKRRLRRGGPNSTFSLLRKELRDGNLQS--LLGGS 135 (223)
Q Consensus 91 i~~qH~~~fk~---~r~rk~rk~~s~s~~s~l~k~lre~~lq~--llggs 135 (223)
+ .|.+.-.- .+.|+.. -+.+.+-.+.+..+|..+++. ++||.
T Consensus 136 ~--~~~a~~r~~~e~~~r~~~-~~r~~g~~lv~~r~rr~~mh~~~s~~g~ 182 (381)
T KOG1280|consen 136 W--TEIALGRPLQDEIGREMA-LLRNMGPDLVEDRRRRTEMHTVPSLPGI 182 (381)
T ss_pred h--hhhcccccchhhhhhhhh-hhccccccccchhhhhhhhheecccCCc
Confidence 3 34333211 1234433 344455555555555544443 34444
No 4
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.14 E-value=0.014 Score=42.28 Aligned_cols=37 Identities=27% Similarity=0.646 Sum_probs=25.3
Q ss_pred CCccceeeCCCCCccchhh--hhhccccccCCCCCCccccCCccCccc
Q 027446 39 DDLNAMFLCPFCAEDFDIV--GLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~~--~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
++..-+|+|| ||..|.++ .| ...-+.++||-|+-.|-
T Consensus 17 e~~~ftyPCP-CGDRFeIsLeDl--------~~GE~VArCPSCSLiv~ 55 (67)
T COG5216 17 EEKTFTYPCP-CGDRFEISLEDL--------RNGEVVARCPSCSLIVC 55 (67)
T ss_pred CCceEEecCC-CCCEeEEEHHHh--------hCCceEEEcCCceEEEE
Confidence 3556799999 99876553 33 22234578999998764
No 5
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.54 E-value=0.031 Score=40.90 Aligned_cols=45 Identities=18% Similarity=0.566 Sum_probs=29.4
Q ss_pred CCCCCC-CCCCccceeeCCCCCccch--hhhhhccccccCCCCCCccccCCccCccc
Q 027446 31 GYDETD-GDDDLNAMFLCPFCAEDFD--IVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 31 ~~~~~~-~d~d~~~~F~CPfC~~~~d--~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
.++|++ ..+....+|||| ||..|. ...|. ..-..+.||-|+-.+.
T Consensus 8 eiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 8 EIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLIIR 55 (67)
T ss_pred EeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEEE
Confidence 456666 334566799999 998644 34442 1233578999998765
No 6
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=93.43 E-value=0.027 Score=31.18 Aligned_cols=23 Identities=30% Similarity=0.674 Sum_probs=14.9
Q ss_pred eeCCCCCcc-chhhhhhccccccC
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDH 67 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH 67 (223)
|.||+|+.. -....|..|+...|
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 678888876 66677777776554
No 7
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=92.02 E-value=0.13 Score=48.97 Aligned_cols=33 Identities=30% Similarity=0.513 Sum_probs=27.4
Q ss_pred eeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCc
Q 027446 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 44 ~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
-=.|-||... +|..+|..||...|- .|-||..+
T Consensus 220 HP~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v 253 (493)
T COG5236 220 HPLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMV 253 (493)
T ss_pred CchhhhccceecChHHHHHHHHhhhh------hhhhhhcc
Confidence 4479999987 999999999998874 57777764
No 8
>PHA00732 hypothetical protein
Probab=91.08 E-value=0.17 Score=37.98 Aligned_cols=42 Identities=31% Similarity=0.723 Sum_probs=33.1
Q ss_pred eeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccchhhhhhh
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHI 91 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~Hi 91 (223)
|.|+.|++. -....|..|+...|.. ..|++|..... ++..|+
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 789999998 5788899998755542 26999999876 577774
No 9
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=91.01 E-value=0.11 Score=37.97 Aligned_cols=47 Identities=26% Similarity=0.567 Sum_probs=13.9
Q ss_pred eCCCCCcc-chhhhhhccccccCCCCCC---------------------ccccCCccCccc--hhhhhhhh
Q 027446 46 LCPFCAED-FDIVGLCCHIDEDHPIEAK---------------------NGVCPVCAKRVG--TDIVSHIT 92 (223)
Q Consensus 46 ~CPfC~~~-~d~~~L~~H~~~eH~~e~k---------------------~~VCPVCa~~v~--~d~i~Hi~ 92 (223)
.|+||+.. -+...|..|+...|.+... .-.|++|..... ..+..||+
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~ 71 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMR 71 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHH
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHc
Confidence 39999998 6788999999999987432 123999999863 68889985
No 10
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=90.84 E-value=0.2 Score=41.23 Aligned_cols=41 Identities=22% Similarity=0.547 Sum_probs=27.9
Q ss_pred CCccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 39 DDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
+.....|.||.|+..|+...-....+ + ....+||.|...+-
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEELE 134 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEEE
Confidence 34577999999998766544333222 2 34489999999864
No 11
>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=90.42 E-value=0.19 Score=31.93 Aligned_cols=34 Identities=21% Similarity=0.410 Sum_probs=21.9
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
.+.||.|+..|.+..-. .......+.||.|...+
T Consensus 2 ~~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEEEeCHHH------cCCCCCEEECCCCCCEE
Confidence 36899999976555431 12223468899998754
No 12
>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=90.36 E-value=0.18 Score=32.10 Aligned_cols=33 Identities=21% Similarity=0.573 Sum_probs=23.6
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
.+|.||-|+..|++..-. .+....+||.|...+
T Consensus 4 Y~y~C~~Cg~~fe~~~~~--------~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKI--------SDDPLATCPECGGDV 36 (41)
T ss_pred EEEEcCCCCCEEEEEEec--------CCCCCCCCCCCCCcc
Confidence 479999999988754331 114567899999843
No 13
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=89.93 E-value=0.14 Score=30.44 Aligned_cols=21 Identities=29% Similarity=0.608 Sum_probs=17.9
Q ss_pred eeeCCCCCccchhhhhhcccc
Q 027446 44 MFLCPFCAEDFDIVGLCCHID 64 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~ 64 (223)
..+||+|+..|-...|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 468999999999999988853
No 14
>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=89.82 E-value=0.083 Score=29.72 Aligned_cols=21 Identities=24% Similarity=0.626 Sum_probs=13.3
Q ss_pred eeCCCCCcc-chhhhhhccccc
Q 027446 45 FLCPFCAED-FDIVGLCCHIDE 65 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~ 65 (223)
|.||.|++. -+...|..|+..
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 567777776 455566666543
No 15
>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=89.51 E-value=0.21 Score=35.22 Aligned_cols=27 Identities=19% Similarity=0.641 Sum_probs=18.0
Q ss_pred CCccccCCccCccc--hhhhhhhhhcccc
Q 027446 71 AKNGVCPVCAKRVG--TDIVSHITMQHGN 97 (223)
Q Consensus 71 ~k~~VCPVCa~~v~--~d~i~Hi~~qH~~ 97 (223)
.....||+|.+.+. .|+-+|+.+.|+.
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 34579999999875 7999999888864
No 16
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=89.50 E-value=0.15 Score=33.54 Aligned_cols=36 Identities=28% Similarity=0.600 Sum_probs=23.6
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhhhhh
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSH 90 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~H 90 (223)
|.||.|+... + +.+ ......||+.|...+..+.+.+
T Consensus 1 m~Cp~Cg~~~-~------~~D---~~~g~~vC~~CG~Vl~e~~i~~ 36 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VFD---PERGELVCPNCGLVLEENIIDE 36 (43)
T ss_dssp ESBTTTSSSE-E------EEE---TTTTEEEETTT-BBEE-TTBSC
T ss_pred CCCcCCcCCc-e------EEc---CCCCeEECCCCCCEeecccccC
Confidence 6899999863 1 121 3456789999988888766643
No 17
>PLN03086 PRLI-interacting factor K; Provisional
Probab=89.30 E-value=0.25 Score=49.34 Aligned_cols=45 Identities=22% Similarity=0.440 Sum_probs=34.5
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc-chhhhhhhh
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV-GTDIVSHIT 92 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v-~~d~i~Hi~ 92 (223)
.-+.||+|++.|....|-.|....| +.+.|| |...+ ..++..|++
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~ 497 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQA 497 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhh
Confidence 3458899999888888999988765 678899 97543 357888864
No 18
>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=89.20 E-value=0.2 Score=35.28 Aligned_cols=31 Identities=19% Similarity=0.559 Sum_probs=22.9
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
.|.||-|+..+++..... .-.+.||.|.+.+
T Consensus 2 ~~~CP~CG~~iev~~~~~---------GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL---------GELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCcc---------CCEEeCCCCCCEE
Confidence 589999999887765421 2257999998863
No 19
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=89.09 E-value=0.16 Score=37.09 Aligned_cols=31 Identities=26% Similarity=0.531 Sum_probs=21.5
Q ss_pred eeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccc
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
-+||||+.+ +.+- |..-...++|.-|.+...
T Consensus 7 KPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 7 KPCPFCGCPSVTVK---------AISGYYRAKCNGCESRTG 38 (64)
T ss_pred cCCCCCCCceeEEE---------ecCceEEEEcCCCCcCcc
Confidence 499999997 5443 222334589999999644
No 20
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.65 E-value=0.15 Score=29.14 Aligned_cols=24 Identities=29% Similarity=0.704 Sum_probs=16.3
Q ss_pred eeCCCCCccchhhhhhccccccCC
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHP 68 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~ 68 (223)
|.||+|+..-....|..|+...|+
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 688999876347788888877664
No 21
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=87.08 E-value=0.41 Score=43.95 Aligned_cols=37 Identities=27% Similarity=0.626 Sum_probs=22.5
Q ss_pred cceeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCc
Q 027446 42 NAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 42 ~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
+..|.||+|++. +.+.+|--||.. |. -.-+|+||-+.
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirT-H~---l~c~C~iCGKa 196 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRT-HT---LPCECGICGKA 196 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhc-cC---CCccccccccc
Confidence 556777777764 777777777664 33 13456666554
No 22
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=86.33 E-value=0.29 Score=33.97 Aligned_cols=31 Identities=26% Similarity=0.526 Sum_probs=18.9
Q ss_pred eeeCCCCCcc-chhhhhhccccccCCCCC---CccccCCccC
Q 027446 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEA---KNGVCPVCAK 81 (223)
Q Consensus 44 ~F~CPfC~~~-~d~~~L~~H~~~eH~~e~---k~~VCPVCa~ 81 (223)
..+|||||.. +.+.. ....+. ..+.|..|.+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 4589999975 43332 111111 4577999987
No 23
>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=86.10 E-value=0.49 Score=31.89 Aligned_cols=32 Identities=19% Similarity=0.678 Sum_probs=22.9
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
.+|.|+-|+..|++.. ...+ ...+.||.|...
T Consensus 4 Yey~C~~Cg~~fe~~~---~~~~-----~~~~~CP~Cg~~ 35 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQ---KMSD-----DPLATCPECGGE 35 (52)
T ss_pred EEEEeCCCCCEeEEEE---ecCC-----CCCCCCCCCCCC
Confidence 4799999999888541 2222 345789999983
No 24
>PHA00733 hypothetical protein
Probab=85.73 E-value=0.73 Score=37.33 Aligned_cols=50 Identities=30% Similarity=0.652 Sum_probs=34.5
Q ss_pred ceeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccc--hhhhhhhhhccc
Q 027446 43 AMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG--TDIVSHITMQHG 96 (223)
Q Consensus 43 ~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~--~d~i~Hi~~qH~ 96 (223)
..|.|+.|+.. -....|..|... | .....|++|..... ..+..|+.--|+
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 35899999987 455667788763 2 23469999988753 578888655443
No 25
>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=85.65 E-value=0.32 Score=30.43 Aligned_cols=24 Identities=29% Similarity=0.913 Sum_probs=12.5
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCccccCCccC
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~ 81 (223)
+||.|+.++.. .|....|||-|..
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 79999987554 4556789999974
No 26
>PHA02768 hypothetical protein; Provisional
Probab=85.40 E-value=0.43 Score=33.87 Aligned_cols=34 Identities=24% Similarity=0.518 Sum_probs=24.0
Q ss_pred eeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccC
Q 027446 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (223)
Q Consensus 44 ~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~ 81 (223)
-|.||.||+. ...+.|..|... |. ++.-|..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~-H~---k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK-HN---TNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh-cC---CcccCCcccc
Confidence 3788888887 667788888887 43 4556666655
No 27
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=84.85 E-value=0.81 Score=42.04 Aligned_cols=84 Identities=27% Similarity=0.377 Sum_probs=52.6
Q ss_pred eeeCCCCCccchhhhh-hccccccCCCCCCccccCCccCccc--hhhhhhhhhcccchhhhcccccccCCCCCcccccch
Q 027446 44 MFLCPFCAEDFDIVGL-CCHIDEDHPIEAKNGVCPVCAKRVG--TDIVSHITMQHGNFFKIQRKRRLRRGGPNSTFSLLR 120 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L-~~H~~~eH~~e~k~~VCPVCa~~v~--~d~i~Hi~~qH~~~fk~~r~rk~rk~~s~s~~s~l~ 120 (223)
-+.|++||+.|+..=| .-|+. .|.. -|+-.||.|..-.. .|+-+||.. |+..=|-+ =.+.-| +-+-.|+|.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiR-THTG-EKPF~C~hC~kAFADRSNLRAHmQT-HS~~K~~q-C~~C~K--sFsl~SyLn 260 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIR-THTG-EKPFSCPHCGKAFADRSNLRAHMQT-HSDVKKHQ-CPRCGK--SFALKSYLN 260 (279)
T ss_pred CcccccccccccchHHhhcccc-cccC-CCCccCCcccchhcchHHHHHHHHh-hcCCcccc-Ccchhh--HHHHHHHHH
Confidence 5899999999997755 45777 4665 46789999999886 599999854 54421211 011111 223356777
Q ss_pred hhhhccccccccC
Q 027446 121 KELRDGNLQSLLG 133 (223)
Q Consensus 121 k~lre~~lq~llg 133 (223)
|-+..|=+-...|
T Consensus 261 KH~ES~C~~~~~g 273 (279)
T KOG2462|consen 261 KHSESACLKYLAG 273 (279)
T ss_pred Hhhhhcccccccc
Confidence 7665554433333
No 28
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=83.65 E-value=0.51 Score=41.22 Aligned_cols=42 Identities=26% Similarity=0.557 Sum_probs=24.8
Q ss_pred eeeCCCCCccchhhhhhc------ccccc--------CCCCCCccccCCccCccch
Q 027446 44 MFLCPFCAEDFDIVGLCC------HIDED--------HPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~------H~~~e--------H~~e~k~~VCPVCa~~v~~ 85 (223)
+++||+|+..|....+.. +.+.+ -|.==...|||-|----..
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 679999999987765433 11111 1111122489999876543
No 29
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.38 E-value=0.66 Score=36.49 Aligned_cols=36 Identities=19% Similarity=0.391 Sum_probs=22.7
Q ss_pred ccceeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccch
Q 027446 41 LNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 41 ~~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
....|.||+|++. +.+. -.+ .---.+||+|-..-+.
T Consensus 18 lpt~f~CP~Cge~~v~v~-------~~k--~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGKVSISVK-------IKK--NIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCCeEeeee-------cCC--CcceEECCCCCCccCE
Confidence 4568999999953 2211 111 1234699999987665
No 30
>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=82.96 E-value=0.67 Score=30.56 Aligned_cols=31 Identities=26% Similarity=0.688 Sum_probs=23.4
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCccC
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~ 81 (223)
.+|.|+-||..|++..- +.+ ...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~---~~~-----~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQS---ISE-----DDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEE---cCC-----CCCCcCCCCCC
Confidence 47999999998877543 221 45789999988
No 31
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=82.75 E-value=0.52 Score=46.00 Aligned_cols=35 Identities=31% Similarity=0.583 Sum_probs=30.7
Q ss_pred CCccceeeCCCCCcc-chhhhhhccccccCCCCCCc
Q 027446 39 DDLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKN 73 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~ 73 (223)
++.+.-|-||+|..+ =....|-+|++.+|..|-..
T Consensus 10 ~~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ed~~ 45 (505)
T KOG1842|consen 10 GEILEGFLCPICLLDLPNLSALNDHLDVEHFEEDEK 45 (505)
T ss_pred chhhhcccCchHhhhhhhHHHHHHHHhhhccccchh
Confidence 577889999999999 46789999999999998764
No 32
>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=82.56 E-value=0.24 Score=36.76 Aligned_cols=55 Identities=20% Similarity=0.411 Sum_probs=28.5
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc-------hhhhhhhhhcccchhhhcc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG-------TDIVSHITMQHGNFFKIQR 103 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~-------~d~i~Hi~~qH~~~fk~~r 103 (223)
..||-|..+++..+-.-||..=+..=.+.+.||-|...+- .|+. =||++-+|+++
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYF----C~~c~gLiSKk 63 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYF----CNHCHGLISKK 63 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-TT
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhccccee----eccCCceeecc
Confidence 4688888887777754444432222234578999999863 3655 45888887643
No 33
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=82.48 E-value=0.92 Score=28.41 Aligned_cols=25 Identities=36% Similarity=0.873 Sum_probs=17.3
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
|.|+-||.-++... .+-+||+|.+.
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCCc
Confidence 67888887655433 45689999763
No 34
>PLN03086 PRLI-interacting factor K; Provisional
Probab=81.43 E-value=1 Score=45.21 Aligned_cols=39 Identities=18% Similarity=0.332 Sum_probs=28.7
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
..+.|| |+..+.-..|-.|+.. |+-. +...|+.|...+.
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~t-hCp~-Kpi~C~fC~~~v~ 515 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQAS-TCPL-RLITCRFCGDMVQ 515 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhhc-cCCC-CceeCCCCCCccc
Confidence 457888 8877888888888764 5543 6678888888763
No 35
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.07 E-value=0.94 Score=30.12 Aligned_cols=29 Identities=21% Similarity=0.610 Sum_probs=19.5
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
+|.||-|+..|+.... . ....||-|..++
T Consensus 3 ~y~C~~CG~~~~~~~~---------~--~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY---------G--TGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC---------C--CceECCCCCCeE
Confidence 6888888887665322 1 157888887654
No 36
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=78.94 E-value=1.1 Score=33.93 Aligned_cols=25 Identities=36% Similarity=0.958 Sum_probs=17.3
Q ss_pred eeCCCCCcc-chhhhhhccccccCCCCCCccccCCcc
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCA 80 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa 80 (223)
|+||-|+.. |+..+ +..--|||||-
T Consensus 2 ~~CPCCg~~Tl~~~~-----------~~~ydIC~VC~ 27 (78)
T PF14206_consen 2 YPCPCCGYYTLEERG-----------EGTYDICPVCF 27 (78)
T ss_pred ccCCCCCcEEeccCC-----------CcCceECCCCC
Confidence 799999975 55432 12245999996
No 37
>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=78.41 E-value=1.6 Score=27.73 Aligned_cols=26 Identities=23% Similarity=0.721 Sum_probs=18.0
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
.|.|+.||.-++... ..-+||||.+.
T Consensus 2 ~~~C~~CG~i~~g~~-------------~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEE-------------APEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCc-------------CCCcCcCCCCc
Confidence 478999997654321 23499999874
No 38
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=77.76 E-value=0.9 Score=36.09 Aligned_cols=37 Identities=19% Similarity=0.401 Sum_probs=23.4
Q ss_pred cceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
.-+|.||||+.+--++-++. -...-.+++|-+|-...
T Consensus 20 ~k~FtCp~Cghe~vs~ctvk-----k~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVK-----KTVNIGTAVCGNCGLSF 56 (104)
T ss_pred CceEecCccCCeeeeEEEEE-----ecCceeEEEcccCcceE
Confidence 45899999998743333311 22334467899998763
No 39
>PF12773 DZR: Double zinc ribbon
Probab=77.10 E-value=1.8 Score=28.82 Aligned_cols=27 Identities=26% Similarity=0.851 Sum_probs=18.1
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
.||.|+..+. ..+...++||.|...+.
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 5777777655 33455678888887654
No 40
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.06 E-value=2 Score=36.71 Aligned_cols=36 Identities=25% Similarity=0.558 Sum_probs=25.7
Q ss_pred CCccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 39 DDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
+.....|.||-|+..|....-.. ..-.||+|...+-
T Consensus 112 e~~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEMLE 147 (178)
T ss_pred ccCCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCCe
Confidence 34568999999998754444322 2679999999865
No 41
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=77.02 E-value=0.92 Score=31.74 Aligned_cols=35 Identities=23% Similarity=0.570 Sum_probs=19.8
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
+.|||||+.+++. .+.-.. ....--=|+||-..+-
T Consensus 1 i~CPyCge~~~~~--iD~s~~---~Q~yiEDC~vCC~PI~ 35 (52)
T PF14255_consen 1 IQCPYCGEPIEIL--IDPSAG---DQEYIEDCQVCCRPIE 35 (52)
T ss_pred CCCCCCCCeeEEE--EecCCC---CeeEEeehhhcCCccE
Confidence 4799999987652 222111 1112234999987643
No 42
>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=76.80 E-value=1.5 Score=29.86 Aligned_cols=25 Identities=12% Similarity=0.211 Sum_probs=15.9
Q ss_pred chhhhhhccccccCCCCCCccccCCccCccch
Q 027446 54 FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 54 ~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
|+...+..++.. ...||+|...+..
T Consensus 23 ~~~~~i~~~~~~-------~~~cP~~~~~~~~ 47 (63)
T smart00504 23 YERRAIEKWLLS-------HGTDPVTGQPLTH 47 (63)
T ss_pred EeHHHHHHHHHH-------CCCCCCCcCCCCh
Confidence 555555555443 4689999987753
No 43
>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=75.96 E-value=2.1 Score=35.72 Aligned_cols=36 Identities=25% Similarity=0.491 Sum_probs=26.7
Q ss_pred CCccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 39 DDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
+.....|.||-|+..|....-.. .+-.||+|...+-
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEee
Confidence 45577999999998755555443 2679999999864
No 44
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=75.27 E-value=2.6 Score=30.54 Aligned_cols=34 Identities=24% Similarity=0.428 Sum_probs=22.1
Q ss_pred CCccceeeCCCCCcc-chh-hhhhccccccCCCCCCccccCCcc
Q 027446 39 DDLNAMFLCPFCAED-FDI-VGLCCHIDEDHPIEAKNGVCPVCA 80 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~-~d~-~~L~~H~~~eH~~e~k~~VCPVCa 80 (223)
+|....|+||-||+. +-. .-...| .+..+||-|-
T Consensus 22 ~e~~v~F~CPnCGe~~I~Rc~~CRk~--------g~~Y~Cp~CG 57 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYRCAKCRKL--------GNPYRCPKCG 57 (61)
T ss_pred CCceeEeeCCCCCceeeehhhhHHHc--------CCceECCCcC
Confidence 456678999999964 433 222222 4467899885
No 45
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=75.02 E-value=2.2 Score=30.72 Aligned_cols=35 Identities=29% Similarity=0.650 Sum_probs=24.4
Q ss_pred CccceeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccC
Q 027446 40 DLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (223)
Q Consensus 40 d~~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~ 81 (223)
+....|.||-||+. +-. |..|.. .+...+||-|--
T Consensus 21 ~~~~~F~CPnCG~~~I~R---C~~CRk----~~~~Y~CP~CGF 56 (59)
T PRK14890 21 EKAVKFLCPNCGEVIIYR---CEKCRK----QSNPYTCPKCGF 56 (59)
T ss_pred CccCEeeCCCCCCeeEee---chhHHh----cCCceECCCCCC
Confidence 44679999999996 443 444543 256789999953
No 46
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=74.74 E-value=1.7 Score=29.58 Aligned_cols=45 Identities=31% Similarity=0.611 Sum_probs=29.8
Q ss_pred eeeCCC--CCccchhhhhhccccccCCCCCCccccCC----ccCccc-hhhhhh
Q 027446 44 MFLCPF--CAEDFDIVGLCCHIDEDHPIEAKNGVCPV----CAKRVG-TDIVSH 90 (223)
Q Consensus 44 ~F~CPf--C~~~~d~~~L~~H~~~eH~~e~k~~VCPV----Ca~~v~-~d~i~H 90 (223)
...||+ |.+.+-...|-.|+..+=+ -+.+.||. |..++. .++..|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~--~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECP--KRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTST--TSEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCC--CCcEECCCCCCCCCCccchhHHhCC
Confidence 578999 7677989999999996433 35789999 999865 456554
No 47
>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=74.32 E-value=1.4 Score=43.19 Aligned_cols=42 Identities=24% Similarity=0.500 Sum_probs=32.7
Q ss_pred ccceeeCCCCCcc-chhhhhhccccccCCCCCCc---cccCCccCc
Q 027446 41 LNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKN---GVCPVCAKR 82 (223)
Q Consensus 41 ~~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~---~VCPVCa~~ 82 (223)
.+.--.||+|.+. .|...+..|+..+|+..-.+ -+.|-+...
T Consensus 54 sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~ 99 (466)
T PF04780_consen 54 SWRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDD 99 (466)
T ss_pred ceeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCH
Confidence 3556789999986 99999999999999987755 355554444
No 48
>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=73.80 E-value=1.5 Score=26.34 Aligned_cols=9 Identities=56% Similarity=1.357 Sum_probs=4.6
Q ss_pred ccCCccCcc
Q 027446 75 VCPVCAKRV 83 (223)
Q Consensus 75 VCPVCa~~v 83 (223)
.||||...+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 355555554
No 49
>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=73.08 E-value=1.8 Score=25.08 Aligned_cols=23 Identities=22% Similarity=0.378 Sum_probs=16.5
Q ss_pred eeCCCCCcc-chhhhhhccccccC
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDH 67 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH 67 (223)
|.|..|++. -+...|..|....|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 678888886 66777777775443
No 50
>PF14353 CpXC: CpXC protein
Probab=72.51 E-value=1.5 Score=34.75 Aligned_cols=38 Identities=24% Similarity=0.657 Sum_probs=21.7
Q ss_pred eeCCCCCccchhhhhhccccc-cCC--------CCCCccccCCccCcc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDE-DHP--------IEAKNGVCPVCAKRV 83 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~-eH~--------~e~k~~VCPVCa~~v 83 (223)
.+||.|+..|+... ...++. ++| .+-...+||-|....
T Consensus 2 itCP~C~~~~~~~v-~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 2 ITCPHCGHEFEFEV-WTSINADEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred cCCCCCCCeeEEEE-EeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 47999998754332 122332 222 233456799998874
No 51
>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=72.01 E-value=2.1 Score=36.32 Aligned_cols=54 Identities=22% Similarity=0.404 Sum_probs=33.1
Q ss_pred ceeeCCC----CCccchhhhhhccccccCCCCCCccccCC----ccCc-cchhhhhhhhhcccchh
Q 027446 43 AMFLCPF----CAEDFDIVGLCCHIDEDHPIEAKNGVCPV----CAKR-VGTDIVSHITMQHGNFF 99 (223)
Q Consensus 43 ~~F~CPf----C~~~~d~~~L~~H~~~eH~~e~k~~VCPV----Ca~~-v~~d~i~Hi~~qH~~~f 99 (223)
-.|+|+| |.+.+-......|... -.-++..||+ |.-. ...++..|++..|....
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 4799999 9999999999999653 3345678999 7542 34699999999998744
No 52
>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=71.98 E-value=2.4 Score=33.59 Aligned_cols=38 Identities=32% Similarity=0.631 Sum_probs=23.8
Q ss_pred eeCCCCCccc---hhhhhhccccccCCCCCCccccCCccCccch
Q 027446 45 FLCPFCAEDF---DIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 45 F~CPfC~~~~---d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
-.||||+... +-..+.-|..++++ ..-||+-|.+.||.
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~---~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGP---YLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCc---eeEECCCCCceeee
Confidence 3799999863 33333333333222 13699999999984
No 53
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=71.60 E-value=2.2 Score=37.32 Aligned_cols=49 Identities=27% Similarity=0.588 Sum_probs=30.1
Q ss_pred CccceeeCCCCCccch--hhhhhccc-----cccCC--------------CCCCccccCCccCccchhhh
Q 027446 40 DLNAMFLCPFCAEDFD--IVGLCCHI-----DEDHP--------------IEAKNGVCPVCAKRVGTDIV 88 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d--~~~L~~H~-----~~eH~--------------~e~k~~VCPVCa~~v~~d~i 88 (223)
+....|.||.|.+.+. +...|-|. -...- ...+...||+|...+..+-+
T Consensus 14 ~~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L 83 (193)
T PLN03208 14 DSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL 83 (193)
T ss_pred cCCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence 3456799999998633 34457772 22110 02234689999999875433
No 54
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=70.93 E-value=1.8 Score=31.48 Aligned_cols=24 Identities=33% Similarity=0.794 Sum_probs=20.2
Q ss_pred eeeCCCCCccc-hhhhhhccccccC
Q 027446 44 MFLCPFCAEDF-DIVGLCCHIDEDH 67 (223)
Q Consensus 44 ~F~CPfC~~~~-d~~~L~~H~~~eH 67 (223)
.|.|++|++.| +...|..|+...|
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 69999999985 8999999999754
No 55
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=70.29 E-value=1.8 Score=32.68 Aligned_cols=36 Identities=31% Similarity=0.597 Sum_probs=14.6
Q ss_pred ccceeeCCCCC-cc-chhhhhhccccccCCCCCCccccCCccCcc
Q 027446 41 LNAMFLCPFCA-ED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 41 ~~~~F~CPfC~-~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
....|.||||+ +. +.+.- +.....-.+.|-+|....
T Consensus 19 l~~~F~CPfC~~~~sV~v~i-------dkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVKI-------DKKEGIGILSCRVCGESF 56 (81)
T ss_dssp -SS----TTT--SS-EEEEE-------ETTTTEEEEEESSS--EE
T ss_pred CCceEcCCcCCCCCeEEEEE-------EccCCEEEEEecCCCCeE
Confidence 34689999999 43 43322 111223345799996653
No 56
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=69.59 E-value=1.3 Score=45.87 Aligned_cols=51 Identities=24% Similarity=0.531 Sum_probs=41.1
Q ss_pred cceeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccc--hhhhhhhh
Q 027446 42 NAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG--TDIVSHIT 92 (223)
Q Consensus 42 ~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~--~d~i~Hi~ 92 (223)
.+..+||||+.. -.+..|..|+.-.|--..-|.-|+.|..... ..+-+|++
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~ 261 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQ 261 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHH
Confidence 356799999996 7788999999999998888899999998754 34555543
No 57
>PRK12495 hypothetical protein; Provisional
Probab=68.51 E-value=2.7 Score=37.61 Aligned_cols=31 Identities=19% Similarity=0.411 Sum_probs=23.0
Q ss_pred cceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccch
Q 027446 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
...|.||.||..|- .+ ...++||+|-..+..
T Consensus 40 msa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGDPIF------------RH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccCccc------------CC-CCeeECCCCCCcccc
Confidence 34789999999843 12 345789999998764
No 58
>PRK12496 hypothetical protein; Provisional
Probab=68.42 E-value=3 Score=35.16 Aligned_cols=27 Identities=22% Similarity=0.565 Sum_probs=19.7
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
.|.|+.|+..|+.. ....+||||-..+
T Consensus 127 ~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~ 153 (164)
T PRK12496 127 RKVCKGCKKKYPED-------------YPDDVCEICGSPV 153 (164)
T ss_pred eEECCCCCccccCC-------------CCCCcCCCCCChh
Confidence 58899999887632 1124899998765
No 59
>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=67.43 E-value=2.1 Score=25.25 Aligned_cols=11 Identities=36% Similarity=1.376 Sum_probs=9.1
Q ss_pred eeeCCCCCccc
Q 027446 44 MFLCPFCAEDF 54 (223)
Q Consensus 44 ~F~CPfC~~~~ 54 (223)
-|+||+|+..|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 39999999765
No 60
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.12 E-value=2.4 Score=36.89 Aligned_cols=43 Identities=23% Similarity=0.602 Sum_probs=26.6
Q ss_pred ceeeCCCCCccchhh----hhhccccccCCC---CCCccccCCccCccch
Q 027446 43 AMFLCPFCAEDFDIV----GLCCHIDEDHPI---EAKNGVCPVCAKRVGT 85 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~----~L~~H~~~eH~~---e~k~~VCPVCa~~v~~ 85 (223)
+.|.||.|=..+..- .=|=|+-=.-|. -.+..+||+|.+++..
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 579999998765433 334443322221 1245689999998874
No 61
>PHA00616 hypothetical protein
Probab=67.08 E-value=1.5 Score=29.76 Aligned_cols=24 Identities=17% Similarity=0.207 Sum_probs=13.7
Q ss_pred eeCCCCCcc-chhhhhhccccccCC
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDHP 68 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH~ 68 (223)
|.||-||.- ..-..|..|+...|-
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg 26 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHK 26 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcC
Confidence 456666665 555556666655443
No 62
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=66.59 E-value=4.5 Score=34.58 Aligned_cols=25 Identities=32% Similarity=0.913 Sum_probs=17.8
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
.+.||-||-- |. . --+.+||||-+.
T Consensus 134 ~~vC~vCGy~--------~~-----g-e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYT--------HE-----G-EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCc--------cc-----C-CCCCcCCCCCCh
Confidence 8999999742 11 1 236799999864
No 63
>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=65.67 E-value=3.9 Score=24.44 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=10.4
Q ss_pred CccceeeCCCCCc
Q 027446 40 DLNAMFLCPFCAE 52 (223)
Q Consensus 40 d~~~~F~CPfC~~ 52 (223)
+....|+||-||+
T Consensus 12 ~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 12 EQAVPFPCPNCGF 24 (24)
T ss_pred ccCceEeCCCCCC
Confidence 4456899999986
No 64
>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=65.40 E-value=2.7 Score=28.83 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=7.4
Q ss_pred eeCCCCCcc
Q 027446 45 FLCPFCAED 53 (223)
Q Consensus 45 F~CPfC~~~ 53 (223)
-+|||||-.
T Consensus 2 kPCPfCGg~ 10 (53)
T TIGR03655 2 KPCPFCGGA 10 (53)
T ss_pred CCCCCCCCc
Confidence 389999974
No 65
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=65.10 E-value=2.8 Score=32.58 Aligned_cols=17 Identities=29% Similarity=0.876 Sum_probs=13.5
Q ss_pred CCccceeeCCCCCcc-ch
Q 027446 39 DDLNAMFLCPFCAED-FD 55 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~-~d 55 (223)
..+.+.|.||||+.+ +.
T Consensus 31 ~~q~a~y~CpfCgk~~vk 48 (90)
T PTZ00255 31 ISQHAKYFCPFCGKHAVK 48 (90)
T ss_pred HHHhCCccCCCCCCCcee
Confidence 467889999999875 44
No 66
>PRK00420 hypothetical protein; Validated
Probab=64.49 E-value=3.5 Score=33.11 Aligned_cols=27 Identities=33% Similarity=0.656 Sum_probs=18.7
Q ss_pred eeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccc
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
-.||.|+.. |.. ....++||+|...+-
T Consensus 24 ~~CP~Cg~pLf~l-------------k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 24 KHCPVCGLPLFEL-------------KDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCCcceec-------------CCCceECCCCCCeee
Confidence 489999976 321 123579999998643
No 67
>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=63.76 E-value=5.9 Score=28.64 Aligned_cols=38 Identities=18% Similarity=0.442 Sum_probs=21.3
Q ss_pred cceeeCCCCCcc------------chhhhhhccccccCCCCCCccccCCccCccch
Q 027446 42 NAMFLCPFCAED------------FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 42 ~~~F~CPfC~~~------------~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
+..|.||.|++- ||...+..++.. ...+||+|...+..
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLSE 51 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-SG
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCCc
Confidence 457888888763 333444444433 57899999887764
No 68
>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=63.08 E-value=2.6 Score=36.00 Aligned_cols=41 Identities=20% Similarity=0.617 Sum_probs=20.7
Q ss_pred cceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
+-.|+||.|+..+...++.. .+.-.....-..||-|.....
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B--
T ss_pred ceEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcCC
Confidence 44899999999988888754 111112344568999999755
No 69
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=62.51 E-value=3 Score=40.57 Aligned_cols=44 Identities=23% Similarity=0.479 Sum_probs=28.8
Q ss_pred CCCCCCCCccceeeCCCCCcc---chhhhhhccccccCCCCCCccccCCccCcc
Q 027446 33 DETDGDDDLNAMFLCPFCAED---FDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 33 ~~~~~d~d~~~~F~CPfC~~~---~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
++...++..++.|.||+|... +|...|..- +...-.|-.|..-+
T Consensus 117 ed~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~-------~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 117 EDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDN-------ETGEFHCENCGGEL 163 (436)
T ss_pred HHHhhhccccccccCCccccchhhhHHHHhhcc-------cCceEEEecCCCch
Confidence 344445677899999999985 666666432 23345788876653
No 70
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=61.94 E-value=3.5 Score=29.21 Aligned_cols=25 Identities=32% Similarity=0.744 Sum_probs=17.1
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
-+||.|++.|... ---||||.|.+-
T Consensus 6 ~~C~~Cg~~~~~~-------------dDiVvCp~Cgap 30 (54)
T PF14446_consen 6 CKCPVCGKKFKDG-------------DDIVVCPECGAP 30 (54)
T ss_pred ccChhhCCcccCC-------------CCEEECCCCCCc
Confidence 4799998876311 124799999874
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.92 E-value=6.2 Score=26.49 Aligned_cols=28 Identities=21% Similarity=0.627 Sum_probs=20.8
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
.|.|.-|+.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58899999987754 23457899997664
No 72
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=61.78 E-value=4 Score=32.42 Aligned_cols=30 Identities=23% Similarity=0.269 Sum_probs=23.4
Q ss_pred CccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
+.+..+.|+-|+..+..... ...||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 56789999999988776543 3579999874
No 73
>smart00355 ZnF_C2H2 zinc finger.
Probab=61.64 E-value=3.8 Score=22.26 Aligned_cols=20 Identities=25% Similarity=0.491 Sum_probs=11.3
Q ss_pred eeCCCCCcc-chhhhhhcccc
Q 027446 45 FLCPFCAED-FDIVGLCCHID 64 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~ 64 (223)
|.|+.|+.. -....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 456666665 44455555554
No 74
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=61.27 E-value=6 Score=33.31 Aligned_cols=34 Identities=32% Similarity=0.730 Sum_probs=19.7
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCc-----cccCCccCccc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKN-----GVCPVCAKRVG 84 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~-----~VCPVCa~~v~ 84 (223)
..||||+.... |+.+.-.....| --||-|....+
T Consensus 1 m~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 1 MRCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred CcCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCcce
Confidence 37999997531 222222222322 35999998865
No 75
>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=60.71 E-value=3.6 Score=32.03 Aligned_cols=15 Identities=33% Similarity=0.977 Sum_probs=12.5
Q ss_pred CCccceeeCCCCCcc
Q 027446 39 DDLNAMFLCPFCAED 53 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~ 53 (223)
..+.+.|+||||+..
T Consensus 30 ~~q~a~y~CpfCgk~ 44 (91)
T TIGR00280 30 IQQKAKYVCPFCGKK 44 (91)
T ss_pred HHHhcCccCCCCCCC
Confidence 457789999999875
No 76
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=60.53 E-value=3.7 Score=31.87 Aligned_cols=17 Identities=24% Similarity=0.794 Sum_probs=13.3
Q ss_pred CCccceeeCCCCCcc-ch
Q 027446 39 DDLNAMFLCPFCAED-FD 55 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~-~d 55 (223)
..+.+.|+||||+.. +.
T Consensus 31 ~~q~a~y~CpfCgk~~vk 48 (90)
T PRK03976 31 EKMRAKHVCPVCGRPKVK 48 (90)
T ss_pred HHHhcCccCCCCCCCceE
Confidence 457789999999875 44
No 77
>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=59.91 E-value=5.3 Score=24.05 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=5.8
Q ss_pred eCCCCCccc
Q 027446 46 LCPFCAEDF 54 (223)
Q Consensus 46 ~CPfC~~~~ 54 (223)
.||-|+..+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 467776665
No 78
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=59.75 E-value=6.7 Score=27.66 Aligned_cols=41 Identities=17% Similarity=0.346 Sum_probs=29.6
Q ss_pred CccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhhhhhh
Q 027446 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHI 91 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~Hi 91 (223)
+.-..=.||.||..... +...+..+||.|-.....|..+=+
T Consensus 24 ~~~TSq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~rD~naA~ 64 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMDRDVNAAR 64 (69)
T ss_pred CCCCccCccCccccccc-----------ccccceEEcCCCCCEECcHHHHHH
Confidence 33467789999976333 345567899999999888877654
No 79
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=59.49 E-value=4.2 Score=23.71 Aligned_cols=8 Identities=38% Similarity=1.319 Sum_probs=4.7
Q ss_pred CCCCCccc
Q 027446 47 CPFCAEDF 54 (223)
Q Consensus 47 CPfC~~~~ 54 (223)
||.|+.++
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 66666553
No 80
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=59.48 E-value=4.7 Score=33.32 Aligned_cols=26 Identities=35% Similarity=0.768 Sum_probs=19.0
Q ss_pred eeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCcc
Q 027446 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 44 ~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
...||-||-. |. | ...++||||-.++
T Consensus 28 ~~hCp~Cg~PLF~------K--------dG~v~CPvC~~~~ 54 (131)
T COG1645 28 AKHCPKCGTPLFR------K--------DGEVFCPVCGYRE 54 (131)
T ss_pred HhhCcccCCccee------e--------CCeEECCCCCceE
Confidence 4789999987 43 1 2358999999653
No 81
>smart00507 HNHc HNH nucleases.
Probab=59.47 E-value=3.4 Score=26.19 Aligned_cols=21 Identities=19% Similarity=0.216 Sum_probs=14.6
Q ss_pred eeCCCCCccchhhhhhccccc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDE 65 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~ 65 (223)
+.|+||+..++...-+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 689999998765344556554
No 82
>PF14279 HNH_5: HNH endonuclease
Probab=59.25 E-value=3.7 Score=30.20 Aligned_cols=44 Identities=20% Similarity=0.567 Sum_probs=26.7
Q ss_pred CCCCCccchhhhh-hccccccC---CCCCCccccCCccCccchhhhhhh
Q 027446 47 CPFCAEDFDIVGL-CCHIDEDH---PIEAKNGVCPVCAKRVGTDIVSHI 91 (223)
Q Consensus 47 CPfC~~~~d~~~L-~~H~~~eH---~~e~k~~VCPVCa~~v~~d~i~Hi 91 (223)
|.||.++++.... .+|+--+= .+..+. ||-.|-..+|...-+++
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN-VCDKCNNKFGSKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc-hhHHHhHHHhHHHHHHH
Confidence 9999998665442 33433210 123445 99999999886444443
No 83
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=59.23 E-value=5.8 Score=26.33 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=16.8
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
.||.||..+-...+- .....|||.|...
T Consensus 2 FCp~Cg~~l~~~~~~---------~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGK---------EKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCC---------CCCEEECCcCCCe
Confidence 589998855333221 1125789999854
No 84
>PF15616 TerY-C: TerY-C metal binding domain
Probab=58.50 E-value=4.5 Score=33.37 Aligned_cols=42 Identities=17% Similarity=0.300 Sum_probs=28.9
Q ss_pred eeCCCCCccchhhhhhccccccCCC-CCCccccCCccCccchhhh
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPI-EAKNGVCPVCAKRVGTDIV 88 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~-e~k~~VCPVCa~~v~~d~i 88 (223)
=.||+|+..+-++.. -|-.-|++ ....++||-|-....-..+
T Consensus 78 PgCP~CGn~~~fa~C--~CGkl~Ci~g~~~~~CPwCg~~g~~~~~ 120 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC--GCGKLFCIDGEGEVTCPWCGNEGSFGAG 120 (131)
T ss_pred CCCCCCcChhcEEEe--cCCCEEEeCCCCCEECCCCCCeeeeccc
Confidence 589999998554432 46666775 3456899999987654443
No 85
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=57.98 E-value=6.4 Score=23.01 Aligned_cols=20 Identities=25% Similarity=0.413 Sum_probs=13.5
Q ss_pred eeCCCCCcc-chhhhhhcccc
Q 027446 45 FLCPFCAED-FDIVGLCCHID 64 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~ 64 (223)
|.|+.|+.. -+...+..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 567777776 66666666654
No 86
>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=57.69 E-value=6.7 Score=38.10 Aligned_cols=35 Identities=31% Similarity=0.848 Sum_probs=17.4
Q ss_pred cceeeCCCCCccchhhhhhccccccCCCCCCccccCCccC-ccchhhhh
Q 027446 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK-RVGTDIVS 89 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~-~v~~d~i~ 89 (223)
.+...||||+..+.. +-+.-+||||-- .||.+.++
T Consensus 378 ~~~v~CP~cgA~y~~-------------~~kG~lC~vC~l~~IG~~a~G 413 (422)
T PF06957_consen 378 SPSVKCPYCGAKYHP-------------EYKGQLCPVCELSEIGADASG 413 (422)
T ss_dssp S-EEE-TTT--EEEG-------------GGTTSB-TTTTTBBTT---S-
T ss_pred CCCeeCCCCCCccCh-------------hhCCCCCCCCcceeeCCccee
Confidence 356789999976432 123569999987 57876655
No 87
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=57.42 E-value=6.3 Score=23.31 Aligned_cols=10 Identities=30% Similarity=1.175 Sum_probs=6.8
Q ss_pred eeCCCCCccc
Q 027446 45 FLCPFCAEDF 54 (223)
Q Consensus 45 F~CPfC~~~~ 54 (223)
-.||.|+..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 3688887754
No 88
>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=56.99 E-value=5.3 Score=32.10 Aligned_cols=25 Identities=24% Similarity=0.792 Sum_probs=16.0
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
+||-|+.++.-. +....|||-|+.-
T Consensus 4 ~CP~C~seytY~------------dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTYH------------DGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceEe------------cCCeeECcccccc
Confidence 688887653211 2345789999864
No 89
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.65 E-value=8.1 Score=31.54 Aligned_cols=43 Identities=26% Similarity=0.492 Sum_probs=24.6
Q ss_pred CccceeeCCCCCccchhhhhhccccc-----cCCC---CCCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDFDIVGLCCHIDE-----DHPI---EAKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~~~L~~H~~~-----eH~~---e~k~~VCPVCa~~ 82 (223)
..+..+.|+-|+..+....-..+++. -|-. ......||.|-..
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 56789999999987655421111111 0111 1234679999864
No 90
>PF13395 HNH_4: HNH endonuclease
Probab=56.51 E-value=5.6 Score=27.29 Aligned_cols=13 Identities=38% Similarity=1.145 Sum_probs=11.4
Q ss_pred CCCCCccchhhhh
Q 027446 47 CPFCAEDFDIVGL 59 (223)
Q Consensus 47 CPfC~~~~d~~~L 59 (223)
||||++.++...|
T Consensus 1 C~Y~g~~i~~~~l 13 (54)
T PF13395_consen 1 CPYCGKPISIENL 13 (54)
T ss_pred CCCCCCCCChhhc
Confidence 9999999888875
No 91
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=55.98 E-value=6.1 Score=25.20 Aligned_cols=20 Identities=20% Similarity=0.501 Sum_probs=9.5
Q ss_pred eeeCCCCCccchhhhhhccc
Q 027446 44 MFLCPFCAEDFDIVGLCCHI 63 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~ 63 (223)
+|.||-|+..+-..-+-.|+
T Consensus 4 ~~~C~nC~R~v~a~RfA~HL 23 (33)
T PF08209_consen 4 YVECPNCGRPVAASRFAPHL 23 (33)
T ss_dssp EEE-TTTSSEEEGGGHHHHH
T ss_pred eEECCCCcCCcchhhhHHHH
Confidence 45555555555444444444
No 92
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=54.89 E-value=6.3 Score=31.23 Aligned_cols=30 Identities=23% Similarity=0.431 Sum_probs=22.2
Q ss_pred CccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
+.+..+.|+-|+..|.+.. ....||.|...
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 5678999999997766543 23469999864
No 93
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=52.91 E-value=2.8 Score=40.33 Aligned_cols=48 Identities=25% Similarity=0.537 Sum_probs=0.0
Q ss_pred eeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccc------hhhhhhhh
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG------TDIVSHIT 92 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~------~d~i~Hi~ 92 (223)
.+||+|++. -.-.-|.+||...--.+.+.--|-.|.++.+ ..+++|++
T Consensus 208 vACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rHvn 262 (467)
T KOG3608|consen 208 VACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRHVN 262 (467)
T ss_pred EecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHhhh
No 94
>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=52.25 E-value=6.9 Score=30.84 Aligned_cols=30 Identities=23% Similarity=0.504 Sum_probs=20.2
Q ss_pred CccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
..+..+.|+-|+..|++.... ..||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~-------------~~CP~Cgs~ 95 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFD-------------FSCPRCGSP 95 (113)
T ss_dssp EE--EEEETTTS-EEECHHCC-------------HH-SSSSSS
T ss_pred ecCCcEECCCCCCEEecCCCC-------------CCCcCCcCC
Confidence 457899999999998776653 239999885
No 95
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=51.90 E-value=3.3 Score=39.60 Aligned_cols=37 Identities=32% Similarity=0.843 Sum_probs=22.0
Q ss_pred CCCCCccchhhh-----------hhccccccCCCCCCccccCCccCccc
Q 027446 47 CPFCAEDFDIVG-----------LCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 47 CPfC~~~~d~~~-----------L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
||.|-|++|+.. +|..|- .|--+.-|+-||.|..+..
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~-~~irq~lngrcpacrr~y~ 64 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCY-NNIRQNLNGRCPACRRKYD 64 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHH-HHHHhhccCCChHhhhhcc
Confidence 777766666542 233222 1223347899999998754
No 96
>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=51.79 E-value=6.1 Score=30.70 Aligned_cols=17 Identities=29% Similarity=0.804 Sum_probs=12.2
Q ss_pred CCccceeeCCCCCcc-ch
Q 027446 39 DDLNAMFLCPFCAED-FD 55 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~-~d 55 (223)
..+...|.||||+.. +.
T Consensus 30 ~~q~~ky~Cp~Cgk~~vk 47 (90)
T PF01780_consen 30 ISQHAKYTCPFCGKTSVK 47 (90)
T ss_dssp HHHHS-BEESSSSSSEEE
T ss_pred HHHhCCCcCCCCCCceeE
Confidence 345678999999986 44
No 97
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.67 E-value=8.2 Score=31.61 Aligned_cols=13 Identities=38% Similarity=1.127 Sum_probs=10.5
Q ss_pred cceeeCCCCCccc
Q 027446 42 NAMFLCPFCAEDF 54 (223)
Q Consensus 42 ~~~F~CPfC~~~~ 54 (223)
...|.||.|+..+
T Consensus 121 ~~~f~Cp~Cg~~l 133 (147)
T smart00531 121 DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEECCCCCCEE
Confidence 3459999999974
No 98
>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=51.42 E-value=7.4 Score=26.37 Aligned_cols=10 Identities=30% Similarity=0.992 Sum_probs=7.0
Q ss_pred cCCccCccch
Q 027446 76 CPVCAKRVGT 85 (223)
Q Consensus 76 CPVCa~~v~~ 85 (223)
||-|..+.+.
T Consensus 1 CP~C~~kkk~ 10 (43)
T PF03470_consen 1 CPFCPGKKKQ 10 (43)
T ss_pred CCCCCCCCCc
Confidence 7777777663
No 99
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=51.00 E-value=5.7 Score=28.71 Aligned_cols=26 Identities=31% Similarity=0.701 Sum_probs=20.0
Q ss_pred ccCCccCcc--chhhhhhhhhcccchhh
Q 027446 75 VCPVCAKRV--GTDIVSHITMQHGNFFK 100 (223)
Q Consensus 75 VCPVCa~~v--~~d~i~Hi~~qH~~~fk 100 (223)
-||-|.+.. .+|.++|.+--|+++|-
T Consensus 19 rCPRC~~~FR~~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 19 RCPRCGMVFRRRKDYIRHVNKAHGWLFG 46 (65)
T ss_pred eCCchhHHHHHhHHHHHHhhHHhhhhhc
Confidence 466666643 47999999999999884
No 100
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=50.40 E-value=8 Score=36.80 Aligned_cols=41 Identities=32% Similarity=0.580 Sum_probs=31.0
Q ss_pred eeeCCC--CCcc-chhhhhhccccccCCC-----------------CCCccccCCccCccc
Q 027446 44 MFLCPF--CAED-FDIVGLCCHIDEDHPI-----------------EAKNGVCPVCAKRVG 84 (223)
Q Consensus 44 ~F~CPf--C~~~-~d~~~L~~H~~~eH~~-----------------e~k~~VCPVCa~~v~ 84 (223)
-|+||. |.+. -.+-+|--|.-.-|+. +.|+.+|+||.++..
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYK 409 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYK 409 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhc
Confidence 489986 7764 7788998888887832 347778999999754
No 101
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=50.37 E-value=5.6 Score=32.03 Aligned_cols=13 Identities=31% Similarity=0.981 Sum_probs=11.1
Q ss_pred CCCCCccchhhhh
Q 027446 47 CPFCAEDFDIVGL 59 (223)
Q Consensus 47 CPfC~~~~d~~~L 59 (223)
||.|+.++-+..|
T Consensus 1 CPvCg~~l~vt~l 13 (113)
T PF09862_consen 1 CPVCGGELVVTRL 13 (113)
T ss_pred CCCCCCceEEEEE
Confidence 9999998877776
No 102
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=50.11 E-value=8.6 Score=38.88 Aligned_cols=53 Identities=25% Similarity=0.497 Sum_probs=34.4
Q ss_pred CCCccceeeCCCCCcc-chhh-hhhcc-----cc---ccCCCCCCccccCCccCccchhhhhh
Q 027446 38 DDDLNAMFLCPFCAED-FDIV-GLCCH-----ID---EDHPIEAKNGVCPVCAKRVGTDIVSH 90 (223)
Q Consensus 38 d~d~~~~F~CPfC~~~-~d~~-~L~~H-----~~---~eH~~e~k~~VCPVCa~~v~~d~i~H 90 (223)
.+|......|-+|... =|-. .=|.| |. .+--.+..|+.||+|...++-|+..|
T Consensus 530 ~~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~ 592 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEP 592 (791)
T ss_pred CccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccch
Confidence 4677778899999975 3322 22333 11 12234778899999999887665555
No 103
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.05 E-value=6.6 Score=36.37 Aligned_cols=43 Identities=30% Similarity=0.487 Sum_probs=27.8
Q ss_pred cceeeCCCCCcc--chhhhh-hccccccCCCCCCc-----cccCCccCccc
Q 027446 42 NAMFLCPFCAED--FDIVGL-CCHIDEDHPIEAKN-----GVCPVCAKRVG 84 (223)
Q Consensus 42 ~~~F~CPfC~~~--~d~~~L-~~H~~~eH~~e~k~-----~VCPVCa~~v~ 84 (223)
...-.||+||+. +--... |.|+-=.-|..+.- ..||-|.+.+-
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 446799999996 555566 77855433333222 37999988653
No 104
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.01 E-value=9.4 Score=33.31 Aligned_cols=40 Identities=18% Similarity=0.412 Sum_probs=29.7
Q ss_pred CCCccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhhhhhhhh
Q 027446 38 DDDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHITM 93 (223)
Q Consensus 38 d~d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~Hi~~ 93 (223)
+++..+.-.||.||. ...+...||.|-...-.|..+=+++
T Consensus 303 ~~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~Ni 342 (364)
T COG0675 303 VPPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALNI 342 (364)
T ss_pred CCCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHHHH
Confidence 344555688999999 2245689999999888888776643
No 105
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=50.01 E-value=9.9 Score=26.26 Aligned_cols=14 Identities=36% Similarity=0.980 Sum_probs=8.8
Q ss_pred CccceeeCCCCCcc
Q 027446 40 DLNAMFLCPFCAED 53 (223)
Q Consensus 40 d~~~~F~CPfC~~~ 53 (223)
+++..|.||-|+..
T Consensus 30 ~Lp~~w~CP~C~a~ 43 (50)
T cd00730 30 DLPDDWVCPVCGAG 43 (50)
T ss_pred HCCCCCCCCCCCCc
Confidence 45566777777653
No 106
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=49.24 E-value=7.8 Score=30.52 Aligned_cols=9 Identities=44% Similarity=1.527 Sum_probs=7.8
Q ss_pred eeeCCCCCc
Q 027446 44 MFLCPFCAE 52 (223)
Q Consensus 44 ~F~CPfC~~ 52 (223)
.++||||++
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 478999998
No 107
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.72 E-value=9.3 Score=36.86 Aligned_cols=15 Identities=27% Similarity=0.747 Sum_probs=11.2
Q ss_pred cceeeCCCCCccchh
Q 027446 42 NAMFLCPFCAEDFDI 56 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~ 56 (223)
..+|+||||..+-+.
T Consensus 372 ~~sfKCPYCP~e~~~ 386 (394)
T KOG2817|consen 372 SQSFKCPYCPVEQLA 386 (394)
T ss_pred CeeeeCCCCCcccCH
Confidence 346999999987443
No 108
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=46.62 E-value=9.8 Score=33.60 Aligned_cols=30 Identities=23% Similarity=0.591 Sum_probs=21.1
Q ss_pred eeeCCCCCccch--hhhhhccccccCCCC-CCccc
Q 027446 44 MFLCPFCAEDFD--IVGLCCHIDEDHPIE-AKNGV 75 (223)
Q Consensus 44 ~F~CPfC~~~~d--~~~L~~H~~~eH~~e-~k~~V 75 (223)
.|.||.|+..+. ..+| +|...|.+| +|.|.
T Consensus 2 ~~~CP~C~~~l~~~~~~~--~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSW--ICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEE--EcCCCCCCccccCce
Confidence 489999999864 3444 567789984 55553
No 109
>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=46.34 E-value=11 Score=31.28 Aligned_cols=41 Identities=27% Similarity=0.605 Sum_probs=28.8
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhhh
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIV 88 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i 88 (223)
..+.|..|+..++...+...+.... ...||.|...+-.|++
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 4689999999888777765554432 2399999997665543
No 110
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.09 E-value=10 Score=38.94 Aligned_cols=28 Identities=36% Similarity=0.571 Sum_probs=24.2
Q ss_pred cceeeCCCCCcc-chhhhhhccccccCCC
Q 027446 42 NAMFLCPFCAED-FDIVGLCCHIDEDHPI 69 (223)
Q Consensus 42 ~~~F~CPfC~~~-~d~~~L~~H~~~eH~~ 69 (223)
+.--.|+||.+. ||...|..|+..+|.+
T Consensus 180 rGhp~C~~C~~~fld~~el~rH~~~~h~~ 208 (669)
T KOG2231|consen 180 RGHPLCKFCHERFLDDDELYRHLRFDHEF 208 (669)
T ss_pred cCCccchhhhhhhccHHHHHHhhccceeh
Confidence 345689999996 9999999999998875
No 111
>PRK03922 hypothetical protein; Provisional
Probab=45.96 E-value=9.2 Score=30.88 Aligned_cols=16 Identities=38% Similarity=0.847 Sum_probs=12.6
Q ss_pred eeeCCCCCccchhhhh
Q 027446 44 MFLCPFCAEDFDIVGL 59 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L 59 (223)
.-.||+|+++|+-+.+
T Consensus 49 ~~~cP~cge~~~~afv 64 (113)
T PRK03922 49 LTICPKCGEPFDSAFV 64 (113)
T ss_pred cccCCCCCCcCCcEEE
Confidence 4589999999986544
No 112
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=45.62 E-value=12 Score=30.11 Aligned_cols=27 Identities=26% Similarity=0.519 Sum_probs=20.7
Q ss_pred ccccCCccCccc-----hhhhhhhhhcccchh
Q 027446 73 NGVCPVCAKRVG-----TDIVSHITMQHGNFF 99 (223)
Q Consensus 73 ~~VCPVCa~~v~-----~d~i~Hi~~qH~~~f 99 (223)
.+.||+|....+ .....||+.-||-.-
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s 56 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISS 56 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhcccccc
Confidence 789999996655 358889888887654
No 113
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=45.05 E-value=9.7 Score=30.23 Aligned_cols=16 Identities=31% Similarity=0.694 Sum_probs=12.6
Q ss_pred eeeCCCCCccchhhhh
Q 027446 44 MFLCPFCAEDFDIVGL 59 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L 59 (223)
.-.||+|+++|+-..+
T Consensus 47 ~~~cP~Cge~~~~a~v 62 (102)
T PF04475_consen 47 DTICPKCGEELDSAFV 62 (102)
T ss_pred cccCCCCCCccCceEE
Confidence 4589999999886544
No 114
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=44.84 E-value=10 Score=35.95 Aligned_cols=12 Identities=42% Similarity=1.018 Sum_probs=10.0
Q ss_pred cceeeCCCCCcc
Q 027446 42 NAMFLCPFCAED 53 (223)
Q Consensus 42 ~~~F~CPfC~~~ 53 (223)
..+|+||||.++
T Consensus 374 ~~~FKCPYCP~~ 385 (396)
T COG5109 374 VLSFKCPYCPEM 385 (396)
T ss_pred cEEeeCCCCCcc
Confidence 457999999886
No 115
>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=44.69 E-value=14 Score=36.76 Aligned_cols=42 Identities=26% Similarity=0.521 Sum_probs=26.8
Q ss_pred cceeeCCCCCccchh--hhhhccccccCCCCCCccccCCccCccch
Q 027446 42 NAMFLCPFCAEDFDI--VGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~--~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
+-..+||-|++.+.+ ..|.- +.+...+.--.+||-|...+..
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w--~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKW--DKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEEccCCCCCCCccccccceee--cCCCCccceEEECCCCcCCCCH
Confidence 456899999997443 34322 2222333444699999998874
No 116
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=44.65 E-value=14 Score=38.24 Aligned_cols=41 Identities=27% Similarity=0.520 Sum_probs=28.9
Q ss_pred CccceeeCCCCCccc----hhhhhhccccccCCCCCCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDF----DIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~----d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
+....+.||.|+..+ +.-.|.||--..| +..+-.||-|...
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 455679999999853 3345666644333 5677899999987
No 117
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=44.60 E-value=7 Score=25.03 Aligned_cols=35 Identities=23% Similarity=0.456 Sum_probs=14.3
Q ss_pred CCCCCccchhh--hhhccccccC---CCCCCc--cccCCccC
Q 027446 47 CPFCAEDFDIV--GLCCHIDEDH---PIEAKN--GVCPVCAK 81 (223)
Q Consensus 47 CPfC~~~~d~~--~L~~H~~~eH---~~e~k~--~VCPVCa~ 81 (223)
|++|+..+... .=+.|+.... ..+..| .+|+.|..
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~ 42 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHR 42 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHH
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHH
Confidence 89999986554 3345554333 222333 35666654
No 118
>PRK04023 DNA polymerase II large subunit; Validated
Probab=44.20 E-value=15 Score=39.63 Aligned_cols=35 Identities=26% Similarity=0.322 Sum_probs=19.7
Q ss_pred CCcccccccCCCCCCChHHHHHHHhHhHHHHHHHH
Q 027446 181 SNENLHERHVQQPPLSDKDQEEKARKSEFVQGLVL 215 (223)
Q Consensus 181 s~~~~~e~~~~~~~ls~ed~eEk~~R~eFVQ~Lll 215 (223)
+++|..|-.+|.--|+..=-+=-.+=|.||-.||-
T Consensus 778 ~~dQivELk~QDiil~~~aa~yll~va~fiDdLL~ 812 (1121)
T PRK04023 778 SEDQIVELKVQDVIISRDAAEYLLRVAKFIDDLLE 812 (1121)
T ss_pred CccceEEeecccEEcchHHHHHHHHHHHHHHHHHH
Confidence 44555565555223444333334567888888874
No 119
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=43.78 E-value=11 Score=27.37 Aligned_cols=46 Identities=20% Similarity=0.399 Sum_probs=21.7
Q ss_pred CccceeeCC--CCCccchhhhhhccccccCC----CCCCccccCCccCccch
Q 027446 40 DLNAMFLCP--FCAEDFDIVGLCCHIDEDHP----IEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 40 d~~~~F~CP--fC~~~~d~~~L~~H~~~eH~----~e~k~~VCPVCa~~v~~ 85 (223)
+..+...|| -|+.-|-..=|...+..... +....|.||.|.+.+.-
T Consensus 16 ~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 16 GEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp -----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 344578887 89888999988888775433 34455679999988753
No 120
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The presence of motifs with seven invariant Cys residues in the N-terminal 50 residues, including three instances of CXXC, would be consistent with function as an oxidoreductase with FeS clusters. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon.
Probab=43.65 E-value=14 Score=35.55 Aligned_cols=35 Identities=20% Similarity=0.419 Sum_probs=24.3
Q ss_pred ceeeCCCCCcc--chhhhh-hccccccCCCCCCccccCCccCcc
Q 027446 43 AMFLCPFCAED--FDIVGL-CCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 43 ~~F~CPfC~~~--~d~~~L-~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
.-..||||+.. -+...| |.||.. .+..||-|....
T Consensus 9 C~~~C~wC~~p~~~~~~~~~c~~C~~------~~~~C~yC~~~~ 46 (404)
T TIGR03278 9 CRGFCRYCYFKKVDDEQPFGCKNCPP------GTKGCDYCTRSV 46 (404)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCcCCC------CCCCCCCCCchh
Confidence 35689999985 444555 777652 367899997763
No 121
>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=43.62 E-value=10 Score=35.53 Aligned_cols=40 Identities=23% Similarity=0.472 Sum_probs=23.8
Q ss_pred eeCCCCCcc-chhh-----------hhhccccccCCCCCCccccCCccCccch
Q 027446 45 FLCPFCAED-FDIV-----------GLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 45 F~CPfC~~~-~d~~-----------~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
+.||.|..+ +--. .+|..|.+.. +....+.||+|...+..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l-~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLL-FVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHH-hcCCCCCCCCCCCccch
Confidence 689999884 2222 2344444443 23345689999887653
No 122
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=43.45 E-value=13 Score=31.70 Aligned_cols=40 Identities=28% Similarity=0.622 Sum_probs=27.0
Q ss_pred eeCCCCCccchhhhhhccccccCCC-----C-CCccccCCccCccc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPI-----E-AKNGVCPVCAKRVG 84 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~-----e-~k~~VCPVCa~~v~ 84 (223)
-.||.|+..++...-..|++-.|+. - -+-+.|+-|....|
T Consensus 21 G~CaiC~~~l~~~~~~~~vDHDH~l~g~~TG~VRGLLC~~CN~~lG 66 (157)
T PHA02565 21 GICPLCKRELDGDVSKNHLDHDHELNGPNAGRVRGLLCNLCNALEG 66 (157)
T ss_pred CcCCCCCCccCCCccccccCCCCCCCCcccccccccCchhhhhhhh
Confidence 4899999987644333477777722 2 24457999998666
No 123
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=42.59 E-value=14 Score=34.09 Aligned_cols=29 Identities=28% Similarity=0.577 Sum_probs=21.9
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
-.+||-|++.+-...|-.. ..|||-|...
T Consensus 27 ~~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEAN----------LNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHhc----------CCCCCCCCCC
Confidence 4699999998766666322 3599999886
No 124
>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=42.32 E-value=13 Score=30.64 Aligned_cols=33 Identities=21% Similarity=0.517 Sum_probs=23.6
Q ss_pred CccceeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccch
Q 027446 40 DLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 40 d~~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
++.....||-|+.. ||+ ...++|||-|..-.-.
T Consensus 5 elGtKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDL-------------NRRPAVSPYTGEQFPP 38 (129)
T ss_pred hhCccccCCCcCcccccc-------------CCCCccCCCcCCccCc
Confidence 45567899999987 553 2347899999876433
No 125
>PRK10220 hypothetical protein; Provisional
Probab=41.80 E-value=12 Score=30.10 Aligned_cols=25 Identities=28% Similarity=0.800 Sum_probs=14.7
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
+||-|+.++.- -+....|||-|+.-
T Consensus 5 ~CP~C~seytY------------~d~~~~vCpeC~hE 29 (111)
T PRK10220 5 HCPKCNSEYTY------------EDNGMYICPECAHE 29 (111)
T ss_pred cCCCCCCcceE------------cCCCeEECCcccCc
Confidence 68888765321 12234688888763
No 126
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=41.48 E-value=15 Score=34.20 Aligned_cols=29 Identities=21% Similarity=0.241 Sum_probs=22.0
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
-.+||-|+..+-...|-. +..|||-|...
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 468999999877766633 24699999875
No 127
>PRK11595 DNA utilization protein GntX; Provisional
Probab=41.38 E-value=14 Score=32.19 Aligned_cols=35 Identities=23% Similarity=0.583 Sum_probs=20.8
Q ss_pred eCCCCCccchh--hhhhccccccCCCCCCccccCCccCc
Q 027446 46 LCPFCAEDFDI--VGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 46 ~CPfC~~~~d~--~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
.|+.|+..+.. ..||.+|...=++- ...||.|...
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg~~ 43 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCGLP 43 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCCCc
Confidence 48888876533 35788776543321 2367777653
No 128
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=41.03 E-value=17 Score=30.86 Aligned_cols=33 Identities=39% Similarity=0.824 Sum_probs=19.7
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCcc-----ccCCccCccc
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNG-----VCPVCAKRVG 84 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~-----VCPVCa~~v~ 84 (223)
.||||+..-..+ ++ .-+.+-.+. .||-|..+.+
T Consensus 2 ~CPfC~~~~tkV-----iD-SR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKV-----ID-SRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCee-----ee-cccccccchhhhhhcccccccccc
Confidence 699998752221 12 223333333 5999999976
No 129
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=40.67 E-value=12 Score=29.96 Aligned_cols=39 Identities=26% Similarity=0.756 Sum_probs=21.4
Q ss_pred ccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 41 LNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 41 ~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
....|.||||.-+= ..-+-++..|- ....-|-||..-..
T Consensus 20 ldt~FnClfcnHek---~v~~~~Dk~~~--iG~~sC~iC~esFq 58 (109)
T KOG3214|consen 20 LDTQFNCLFCNHEK---SVSCTLDKKHN--IGKASCRICEESFQ 58 (109)
T ss_pred hheeeccCcccccc---ceeeeehhhcC--cceeeeeehhhhhc
Confidence 34579999998652 11111222222 23456999987544
No 130
>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=40.60 E-value=16 Score=33.65 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=21.7
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
-.+||-|++.+-...|-. +..|||-|...
T Consensus 26 ~~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELER----------NLEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHh----------hCCCCCCCCCc
Confidence 468999999876666532 24699999886
No 131
>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=40.19 E-value=20 Score=30.15 Aligned_cols=33 Identities=24% Similarity=0.594 Sum_probs=19.3
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCcc-----ccCCccCccc
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNG-----VCPVCAKRVG 84 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~-----VCPVCa~~v~ 84 (223)
.||||+.+=+- +.+.-+.+-.+. -|+.|..+.+
T Consensus 2 ~CP~C~~~dtk------ViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTR------VLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCE------eeeccccCCCCeeeecccCCccCCccc
Confidence 69999974211 112223333333 4999999876
No 132
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=39.67 E-value=16 Score=25.62 Aligned_cols=9 Identities=33% Similarity=1.409 Sum_probs=8.2
Q ss_pred eeeCCCCCc
Q 027446 44 MFLCPFCAE 52 (223)
Q Consensus 44 ~F~CPfC~~ 52 (223)
.|.||+|+.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 899999985
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=39.27 E-value=15 Score=26.17 Aligned_cols=18 Identities=28% Similarity=0.678 Sum_probs=12.2
Q ss_pred eeeCCCCCccchhhhhhc
Q 027446 44 MFLCPFCAEDFDIVGLCC 61 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~ 61 (223)
.-.||+|...+|...|+.
T Consensus 7 iL~Cp~ck~pL~~~~l~~ 24 (68)
T PF03966_consen 7 ILACPVCKGPLDWEALVE 24 (68)
T ss_dssp TBB-TTTSSBEHHHHHHH
T ss_pred hhcCCCCCCcchHHHHHH
Confidence 358999988886666554
No 134
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=39.11 E-value=8.5 Score=29.81 Aligned_cols=15 Identities=27% Similarity=0.758 Sum_probs=12.4
Q ss_pred CCccceeeCCCCCcc
Q 027446 39 DDLNAMFLCPFCAED 53 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~ 53 (223)
.-+.+.|.|+|||..
T Consensus 31 i~Qhaky~CsfCGK~ 45 (92)
T KOG0402|consen 31 IQQHAKYTCSFCGKK 45 (92)
T ss_pred HHHhhhhhhhhcchh
Confidence 346789999999986
No 135
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=38.91 E-value=10 Score=29.45 Aligned_cols=38 Identities=29% Similarity=0.672 Sum_probs=11.4
Q ss_pred eCCCCCccchhhhhh-ccccccCCC-----------CCCccccCCccCcc
Q 027446 46 LCPFCAEDFDIVGLC-CHIDEDHPI-----------EAKNGVCPVCAKRV 83 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~-~H~~~eH~~-----------e~k~~VCPVCa~~v 83 (223)
.||+|++.+....+. .=|..-|.+ +++.-+|++|..+.
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 799999976644432 336666655 45556899998764
No 136
>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=38.70 E-value=13 Score=25.38 Aligned_cols=12 Identities=33% Similarity=0.927 Sum_probs=5.2
Q ss_pred eCCCCCccchhh
Q 027446 46 LCPFCAEDFDIV 57 (223)
Q Consensus 46 ~CPfC~~~~d~~ 57 (223)
.||.|+.+||..
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 677777766644
No 137
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=38.66 E-value=17 Score=23.59 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=7.6
Q ss_pred CCccccCCcc
Q 027446 71 AKNGVCPVCA 80 (223)
Q Consensus 71 ~k~~VCPVCa 80 (223)
.+.++||+|.
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 5568899985
No 138
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=38.46 E-value=23 Score=24.18 Aligned_cols=33 Identities=18% Similarity=0.560 Sum_probs=21.2
Q ss_pred CCccceeeCCCCCccchhhhhhccccccCCCCCCccccCCc
Q 027446 39 DDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVC 79 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVC 79 (223)
......+.||.|+.++....= .+. .+...||.|
T Consensus 23 s~~~v~W~C~~Cgh~w~~~v~-------~R~-~~~~~CP~C 55 (55)
T PF14311_consen 23 SNKKVWWKCPKCGHEWKASVN-------DRT-RRGKGCPYC 55 (55)
T ss_pred CCCEEEEECCCCCCeeEccHh-------hhc-cCCCCCCCC
Confidence 345667999999887554321 111 456789988
No 139
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=38.22 E-value=30 Score=22.05 Aligned_cols=32 Identities=25% Similarity=0.661 Sum_probs=18.8
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
..||-|+..|.+..=. + +...+.+-||.|...
T Consensus 3 i~CP~C~~~f~v~~~~--l----~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK--L----PAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHH--c----ccCCcEEECCCCCcE
Confidence 5788888865443310 0 233556778888653
No 140
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=38.21 E-value=9.9 Score=36.43 Aligned_cols=30 Identities=23% Similarity=0.433 Sum_probs=26.0
Q ss_pred eeeCCCCCccch-hhhhhccccccCCCCCCc
Q 027446 44 MFLCPFCAEDFD-IVGLCCHIDEDHPIEAKN 73 (223)
Q Consensus 44 ~F~CPfC~~~~d-~~~L~~H~~~eH~~e~k~ 73 (223)
...|=||..-.| .+.|..|+.+.|.++-..
T Consensus 279 ~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~K 309 (423)
T KOG2482|consen 279 SVVCLFCTNFYENPVFLFEHMKIVHEFDLLK 309 (423)
T ss_pred ceEEEeeccchhhHHHHHHHHHHHHHhhHHh
Confidence 489999998777 999999999999997643
No 141
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=37.84 E-value=26 Score=22.33 Aligned_cols=31 Identities=23% Similarity=0.642 Sum_probs=19.0
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccC
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~ 81 (223)
+.||-|...|++..- .=+-....+-||.|..
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 578888886555432 1133455677888864
No 142
>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=36.82 E-value=19 Score=23.87 Aligned_cols=11 Identities=27% Similarity=1.222 Sum_probs=8.8
Q ss_pred eeeCCCCCccc
Q 027446 44 MFLCPFCAEDF 54 (223)
Q Consensus 44 ~F~CPfC~~~~ 54 (223)
.-.||||+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 67999999753
No 143
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=36.59 E-value=20 Score=34.11 Aligned_cols=39 Identities=33% Similarity=0.713 Sum_probs=27.7
Q ss_pred ceeeCCCCCccch--hhhhhcccccc-CCC-----CCCccccCCccC
Q 027446 43 AMFLCPFCAEDFD--IVGLCCHIDED-HPI-----EAKNGVCPVCAK 81 (223)
Q Consensus 43 ~~F~CPfC~~~~d--~~~L~~H~~~e-H~~-----e~k~~VCPVCa~ 81 (223)
.+-.||.||...| +.+||.=|.-+ |+. +.+-.+|+-|-+
T Consensus 5 ~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 5 STILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred cccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCC
Confidence 4668999999988 78888766554 443 333457888875
No 144
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=36.50 E-value=11 Score=26.05 Aligned_cols=33 Identities=24% Similarity=0.550 Sum_probs=12.1
Q ss_pred cceeeCCCCCccchhhhhhccccccCCCCCCccccCCccC
Q 027446 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~ 81 (223)
..-++|| |+..+=.-- ..++. +..+++||-|..
T Consensus 13 ~~~~PC~-Cgf~IC~~C-~~~i~-----~~~~g~CPgCr~ 45 (48)
T PF14570_consen 13 KDFYPCE-CGFQICRFC-YHDIL-----ENEGGRCPGCRE 45 (48)
T ss_dssp TT--SST-TS----HHH-HHHHT-----TSS-SB-TTT--
T ss_pred CccccCc-CCCcHHHHH-HHHHH-----hccCCCCCCCCC
Confidence 3567887 776532211 11122 234789999965
No 145
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=35.22 E-value=8.9 Score=23.30 Aligned_cols=11 Identities=27% Similarity=0.942 Sum_probs=7.6
Q ss_pred CccccCCccCc
Q 027446 72 KNGVCPVCAKR 82 (223)
Q Consensus 72 k~~VCPVCa~~ 82 (223)
.+..||+|...
T Consensus 34 ~~~~Cp~C~~~ 44 (45)
T cd00162 34 GKNTCPLCRTP 44 (45)
T ss_pred CcCCCCCCCCc
Confidence 35679998754
No 146
>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=34.37 E-value=13 Score=32.36 Aligned_cols=19 Identities=21% Similarity=0.447 Sum_probs=0.0
Q ss_pred eeCCCCCccchhhhhhccc
Q 027446 45 FLCPFCAEDFDIVGLCCHI 63 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~ 63 (223)
..||.||+.+-+..+-.|+
T Consensus 169 ~~cPitGe~IP~~e~~eHm 187 (229)
T PF12230_consen 169 IICPITGEMIPADEMDEHM 187 (229)
T ss_dssp -------------------
T ss_pred ccccccccccccccccccc
Confidence 3444444444444444443
No 147
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.37 E-value=17 Score=27.74 Aligned_cols=45 Identities=24% Similarity=0.521 Sum_probs=31.5
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhhhhhhhhcccchhh
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHITMQHGNFFK 100 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~Hi~~qH~~~fk 100 (223)
..|.|--|+..+|+.- |+.+ .-.+.||-|.+++.+-|- .-|-.||
T Consensus 11 Y~Y~c~~cg~~~dvvq---~~~d-----dplt~ce~c~a~~kk~l~-----~vgi~fK 55 (82)
T COG2331 11 YSYECTECGNRFDVVQ---AMTD-----DPLTTCEECGARLKKLLN-----AVGIVFK 55 (82)
T ss_pred eEEeecccchHHHHHH---hccc-----CccccChhhChHHHHhhc-----cceEEEe
Confidence 4799999999998753 4443 445799999998776442 2345566
No 148
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=34.25 E-value=23 Score=34.95 Aligned_cols=16 Identities=44% Similarity=0.885 Sum_probs=13.7
Q ss_pred CCCCccccCCccCccc
Q 027446 69 IEAKNGVCPVCAKRVG 84 (223)
Q Consensus 69 ~e~k~~VCPVCa~~v~ 84 (223)
.+++.-|||||...||
T Consensus 33 ~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 33 AEPNTNVCPVCLGLPG 48 (474)
T ss_pred CCCCCCcCccccCCCC
Confidence 4567889999999988
No 149
>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=33.97 E-value=17 Score=25.36 Aligned_cols=44 Identities=16% Similarity=0.279 Sum_probs=27.3
Q ss_pred CCCCCCCC-CccceeeCCCCCcc--chhhhhhccccccCCCCCCccccCCccCccc
Q 027446 32 YDETDGDD-DLNAMFLCPFCAED--FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 32 ~~~~~~d~-d~~~~F~CPfC~~~--~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
+++++.++ +..-.|+|+ ||-. +....|-.+ .--+.|+-|+-.+.
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 44544332 335789995 9986 566666444 23467999998764
No 150
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=33.88 E-value=26 Score=38.55 Aligned_cols=35 Identities=29% Similarity=0.317 Sum_probs=20.3
Q ss_pred CCcccccccCCCCCCChHHHHHHHhHhHHHHHHHH
Q 027446 181 SNENLHERHVQQPPLSDKDQEEKARKSEFVQGLVL 215 (223)
Q Consensus 181 s~~~~~e~~~~~~~ls~ed~eEk~~R~eFVQ~Lll 215 (223)
.++|..|-.+|.--|+..=-+=-.+=|.||-.||-
T Consensus 825 ~~dQivELk~QDiil~~~aa~yl~~va~fiDdLL~ 859 (1337)
T PRK14714 825 HEDQVVELKVQDIVLSDGAAEYLLKVAKFVDDLLE 859 (1337)
T ss_pred CccceEEeecccEEcchHHHHHHHHHHHHHHHHHH
Confidence 44555565555223554444444667889988874
No 151
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=33.73 E-value=20 Score=28.42 Aligned_cols=31 Identities=19% Similarity=0.499 Sum_probs=21.4
Q ss_pred CccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
..+..+.|+-|+..|..... ....||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQ------------RVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCCeeecCCc------------cCCcCcCcCCC
Confidence 56789999999975544322 11469999864
No 152
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=33.59 E-value=17 Score=34.44 Aligned_cols=41 Identities=27% Similarity=0.502 Sum_probs=25.0
Q ss_pred eeeCCCCCccchhhhhhccccccC-CCCCCccccCCccCccc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDH-PIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH-~~e~k~~VCPVCa~~v~ 84 (223)
.-.||+|+..---...|++|-... +.+..+.+|.+|...+.
T Consensus 136 ~g~CP~C~~~~a~g~~Ce~cG~~~~~~~l~~p~~~~~g~~~~ 177 (391)
T PF09334_consen 136 EGTCPYCGSDKARGDQCENCGRPLEPEELINPVCKICGSPPE 177 (391)
T ss_dssp TCEETTT--SSCTTTEETTTSSBEECCCSECEEETTTS-B-E
T ss_pred eccccCcCccccCCCcccCCCCCcccccccCCccccccccCc
Confidence 357999986544456666665322 45778889999988754
No 153
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=33.59 E-value=28 Score=30.05 Aligned_cols=32 Identities=28% Similarity=0.626 Sum_probs=23.3
Q ss_pred ccceeeCCCCCcc--chhhhhhccccccCCCCCCccccCCccCccc
Q 027446 41 LNAMFLCPFCAED--FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 41 ~~~~F~CPfC~~~--~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
....|.||-|... ||.+.+ + .-.||.|.+.+-
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~--~----------~F~Cp~Cg~~L~ 143 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAME--L----------GFTCPKCGEDLE 143 (176)
T ss_pred cCCceeCCCCCCcccHHHHHH--h----------CCCCCCCCchhh
Confidence 4457999999886 555544 2 268999999764
No 154
>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=33.46 E-value=22 Score=21.40 Aligned_cols=20 Identities=25% Similarity=0.760 Sum_probs=10.7
Q ss_pred eeCCCCCccch-hhhhhcccc
Q 027446 45 FLCPFCAEDFD-IVGLCCHID 64 (223)
Q Consensus 45 F~CPfC~~~~d-~~~L~~H~~ 64 (223)
|.|.+|+..|. ...+..|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 55666666543 444555543
No 155
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=33.31 E-value=14 Score=32.18 Aligned_cols=20 Identities=15% Similarity=0.586 Sum_probs=0.0
Q ss_pred cccCCccCccc-hhhhhhhhh
Q 027446 74 GVCPVCAKRVG-TDIVSHITM 93 (223)
Q Consensus 74 ~VCPVCa~~v~-~d~i~Hi~~ 93 (223)
.+||||..+|- ..|-.||++
T Consensus 169 ~~cPitGe~IP~~e~~eHmRi 189 (229)
T PF12230_consen 169 IICPITGEMIPADEMDEHMRI 189 (229)
T ss_dssp ---------------------
T ss_pred ccccccccccccccccccccc
Confidence 69999999965 589999764
No 156
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=33.16 E-value=18 Score=27.46 Aligned_cols=18 Identities=33% Similarity=0.755 Sum_probs=10.7
Q ss_pred CCccceeeCCCCCccchh
Q 027446 39 DDLNAMFLCPFCAEDFDI 56 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~ 56 (223)
-|+-+.|.||-|++.+++
T Consensus 60 VENMs~~~Cp~Cg~~~~i 77 (81)
T PF10609_consen 60 VENMSYFVCPHCGERIYI 77 (81)
T ss_dssp EECT-EEE-TTT--EEET
T ss_pred EECCCccCCCCCCCeecC
Confidence 467789999999987543
No 157
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=33.02 E-value=21 Score=25.41 Aligned_cols=13 Identities=31% Similarity=0.649 Sum_probs=10.3
Q ss_pred ccceeeCCCCCcc
Q 027446 41 LNAMFLCPFCAED 53 (223)
Q Consensus 41 ~~~~F~CPfC~~~ 53 (223)
.+..|.||.||..
T Consensus 11 ~~v~~~Cp~cGip 23 (55)
T PF13824_consen 11 AHVNFECPDCGIP 23 (55)
T ss_pred cccCCcCCCCCCc
Confidence 3568999999865
No 158
>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=32.95 E-value=22 Score=25.86 Aligned_cols=11 Identities=36% Similarity=0.987 Sum_probs=8.1
Q ss_pred cceeeCCCCCc
Q 027446 42 NAMFLCPFCAE 52 (223)
Q Consensus 42 ~~~F~CPfC~~ 52 (223)
...+.|-+||+
T Consensus 3 k~~~~C~~Cg~ 13 (69)
T PF09706_consen 3 KKKYNCIFCGE 13 (69)
T ss_pred CCCCcCcCCCC
Confidence 34678999994
No 159
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.90 E-value=7.4 Score=32.24 Aligned_cols=39 Identities=31% Similarity=0.526 Sum_probs=23.5
Q ss_pred cceeeCCCCCccchhh-hh-hccccccCCCCC---CccccCCcc
Q 027446 42 NAMFLCPFCAEDFDIV-GL-CCHIDEDHPIEA---KNGVCPVCA 80 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~~-~L-~~H~~~eH~~e~---k~~VCPVCa 80 (223)
...+.||.|.+.|... .| |-|---..+... ....||+|.
T Consensus 11 ~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 11 QEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred cccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccC
Confidence 3578999999987666 23 333222222222 337899999
No 160
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.68 E-value=24 Score=28.08 Aligned_cols=31 Identities=29% Similarity=0.598 Sum_probs=22.0
Q ss_pred CccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
+.+..+.|+-|+..+..... ....||-|...
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 56789999999977655422 12359999874
No 161
>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=32.65 E-value=27 Score=30.68 Aligned_cols=23 Identities=17% Similarity=0.257 Sum_probs=14.4
Q ss_pred CCCChHHHHHHHhHhHHH-HHHHH
Q 027446 193 PPLSDKDQEEKARKSEFV-QGLVL 215 (223)
Q Consensus 193 ~~ls~ed~eEk~~R~eFV-Q~Lll 215 (223)
-.++++|.++-.+++.++ -+|+.
T Consensus 145 r~~~~~e~~~~~~~~~~~le~l~~ 168 (236)
T PF04981_consen 145 RKLTEEEKEVIHKIVFEILEQLIL 168 (236)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHh
Confidence 358888887766666654 34433
No 162
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=32.07 E-value=23 Score=32.89 Aligned_cols=28 Identities=32% Similarity=0.616 Sum_probs=21.1
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
-+||-|++.+=..+|- .+..|||-|...
T Consensus 29 ~KCp~c~~~~y~~eL~----------~n~~vcp~c~~h 56 (294)
T COG0777 29 TKCPSCGEMLYRKELE----------SNLKVCPKCGHH 56 (294)
T ss_pred eECCCccceeeHHHHH----------hhhhcccccCcc
Confidence 4899999976555553 345699999886
No 163
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.97 E-value=16 Score=35.29 Aligned_cols=46 Identities=24% Similarity=0.483 Sum_probs=27.5
Q ss_pred CCccceeeCCCCCccchhhh--hhccccccCCCC---CCccccCCccCccc
Q 027446 39 DDLNAMFLCPFCAEDFDIVG--LCCHIDEDHPIE---AKNGVCPVCAKRVG 84 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~~~--L~~H~~~eH~~e---~k~~VCPVCa~~v~ 84 (223)
+++...|.||.|...|.... =|.|.-=..|.. .....||+|...++
T Consensus 21 ~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred cccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 34556789999998765443 344432211211 12357999998765
No 164
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=31.85 E-value=21 Score=23.94 Aligned_cols=26 Identities=23% Similarity=0.584 Sum_probs=15.2
Q ss_pred ceeeCCCCCccchhh------hhhccccccCC
Q 027446 43 AMFLCPFCAEDFDIV------GLCCHIDEDHP 68 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~------~L~~H~~~eH~ 68 (223)
+.-.|-+|+..+... .|..|+...|+
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 566777777765443 45555554443
No 165
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=31.54 E-value=11 Score=25.95 Aligned_cols=30 Identities=20% Similarity=0.641 Sum_probs=18.2
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
.|+.|+.++-.-.- -.+.+ . .||.-|..++
T Consensus 1 ~C~iCg~kigl~~~-~k~~D-----G--~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR-FKIKD-----G--YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc-eeccC-----c--cchHHHHHHh
Confidence 48888887544332 12222 2 4899888776
No 166
>PHA02929 N1R/p28-like protein; Provisional
Probab=31.51 E-value=11 Score=33.82 Aligned_cols=42 Identities=24% Similarity=0.379 Sum_probs=24.8
Q ss_pred ceeeCCCCCccchhh----------hhhccccccCCC---CCCccccCCccCccc
Q 027446 43 AMFLCPFCAEDFDIV----------GLCCHIDEDHPI---EAKNGVCPVCAKRVG 84 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~----------~L~~H~~~eH~~---e~k~~VCPVCa~~v~ 84 (223)
....||.|.+.+... .=|.|.--..|. -.....||+|...+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 456999999974321 125554322222 124568999998654
No 167
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=31.49 E-value=20 Score=30.89 Aligned_cols=14 Identities=43% Similarity=0.921 Sum_probs=11.6
Q ss_pred eeCCCCCccchhhh
Q 027446 45 FLCPFCAEDFDIVG 58 (223)
Q Consensus 45 F~CPfC~~~~d~~~ 58 (223)
=+||+|+..+|-.+
T Consensus 155 P~CPlCg~PlDP~G 168 (171)
T PF11290_consen 155 PPCPLCGEPLDPEG 168 (171)
T ss_pred CCCCCCCCCCCCCC
Confidence 57999999988654
No 168
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=31.35 E-value=41 Score=30.83 Aligned_cols=40 Identities=28% Similarity=0.587 Sum_probs=28.6
Q ss_pred ccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhhhhh
Q 027446 41 LNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSH 90 (223)
Q Consensus 41 ~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~H 90 (223)
......||.|+.. .+ +.+ ++....||.-|-.-+..++|.+
T Consensus 8 ~~~~~~Cp~Cg~~----~i---v~d---~~~Ge~vC~~CG~Vl~e~~iD~ 47 (310)
T PRK00423 8 EEEKLVCPECGSD----KL---IYD---YERGEIVCADCGLVIEENIIDQ 47 (310)
T ss_pred cccCCcCcCCCCC----Ce---eEE---CCCCeEeecccCCccccccccc
Confidence 3334589999962 11 222 3567899999999999999876
No 169
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=30.90 E-value=32 Score=33.51 Aligned_cols=43 Identities=23% Similarity=0.427 Sum_probs=24.2
Q ss_pred CccceeeCCCCCccchhhhhhc--cccccCCCC--CCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDFDIVGLCC--HIDEDHPIE--AKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~~~L~~--H~~~eH~~e--~k~~VCPVCa~~ 82 (223)
+....|.|+.|+-.+|...--. -+..-=+++ +-.-+||+|...
T Consensus 421 ~~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 421 DLGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 3456899999998787653210 011001111 124589999875
No 170
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=30.89 E-value=35 Score=31.44 Aligned_cols=36 Identities=25% Similarity=0.542 Sum_probs=26.2
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhhhhh
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSH 90 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~H 90 (223)
..||.|+.. + +..+ ++....||--|-.-+..+.|.+
T Consensus 2 ~~CpeCg~~-~-------~~~d--~~~ge~VC~~CG~Vi~~~~id~ 37 (285)
T COG1405 2 MSCPECGST-N-------IITD--YERGEIVCADCGLVLEDSLIDP 37 (285)
T ss_pred CCCCCCCCc-c-------ceee--ccCCeEEeccCCEEeccccccC
Confidence 379999987 1 1111 3355789999999999888876
No 171
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=30.75 E-value=18 Score=23.30 Aligned_cols=27 Identities=33% Similarity=0.816 Sum_probs=15.5
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCccccCCccC
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~ 81 (223)
.||-|+..+....+ .+..--+||-|.-
T Consensus 1 ~CP~C~~~l~~~~~---------~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGTELEPVRL---------GDVEIDVCPSCGG 27 (41)
T ss_pred CcCCCCcccceEEE---------CCEEEEECCCCCe
Confidence 48888776665554 1122236777754
No 172
>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=30.53 E-value=32 Score=31.93 Aligned_cols=26 Identities=35% Similarity=0.732 Sum_probs=17.2
Q ss_pred hhccccccCCCCCCccccCCccCccc
Q 027446 59 LCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 59 L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
|.|.|-.+...+++.-|||||...||
T Consensus 18 lFc~c~~~~~~~pNt~v~~~~lg~PG 43 (289)
T PF02934_consen 18 LFCSCPNEFGAEPNTNVCPVCLGLPG 43 (289)
T ss_dssp SSSSSBSSTTSCTTSSB-TTTTT-TT
T ss_pred CCCCCCCCCCCCCccccCceeccCCC
Confidence 34445555555788899999999988
No 173
>PF14968 CCDC84: Coiled coil protein 84
Probab=30.29 E-value=29 Score=32.88 Aligned_cols=26 Identities=23% Similarity=0.478 Sum_probs=19.9
Q ss_pred CCccceeeCCCCCccchhh-------hhhcccc
Q 027446 39 DDLNAMFLCPFCAEDFDIV-------GLCCHID 64 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~~-------~L~~H~~ 64 (223)
.+.+..|=|+||+.++... ++..|+-
T Consensus 53 ~~~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLa 85 (336)
T PF14968_consen 53 PEHRNRFWCVFCDCEVREHDSSFACGGAIEHLA 85 (336)
T ss_pred ccccceeEeeCccchhhhccchhhhccHHhhcC
Confidence 4667899999999997655 6666664
No 174
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.09 E-value=18 Score=26.58 Aligned_cols=50 Identities=24% Similarity=0.572 Sum_probs=31.6
Q ss_pred eeCCCCCc--cchhhhhhccccccCCCCCCccccCCccCccchhhhhhhhhcccch
Q 027446 45 FLCPFCAE--DFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHITMQHGNF 98 (223)
Q Consensus 45 F~CPfC~~--~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~Hi~~qH~~~ 98 (223)
.+|-.|+. .+|...+-.---..-| -+...||-|..++..--+.. ++||++
T Consensus 3 vkCiiCd~v~~iD~rt~~tKrLrN~P--IrtymC~eC~~Rva~kt~~R--~~~g~f 54 (68)
T COG4896 3 VKCIICDRVDEIDNRTFKTKRLRNKP--IRTYMCPECEHRVAIKTISR--VNSGHF 54 (68)
T ss_pred ceEEEecceeeecchhHHHHHhhCCC--ceeEechhhHhhhchhhHHH--hccCCc
Confidence 36777876 2666666444333323 34458999999988666655 677765
No 175
>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=29.90 E-value=17 Score=23.39 Aligned_cols=14 Identities=14% Similarity=0.498 Sum_probs=5.5
Q ss_pred ceeeCCCCCccchh
Q 027446 43 AMFLCPFCAEDFDI 56 (223)
Q Consensus 43 ~~F~CPfC~~~~d~ 56 (223)
....|-||+..+..
T Consensus 15 ~~a~C~~C~~~~~~ 28 (45)
T PF02892_consen 15 KKAKCKYCGKVIKY 28 (45)
T ss_dssp S-EEETTTTEE---
T ss_pred CeEEeCCCCeEEee
Confidence 34456666554433
No 176
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=29.89 E-value=20 Score=24.44 Aligned_cols=15 Identities=33% Similarity=0.957 Sum_probs=9.3
Q ss_pred CCccceeeCCCCCcc
Q 027446 39 DDLNAMFLCPFCAED 53 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~ 53 (223)
++++..|.||-|+..
T Consensus 29 ~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 29 EDLPDDWVCPVCGAP 43 (47)
T ss_dssp GGS-TT-B-TTTSSB
T ss_pred HHCCCCCcCcCCCCc
Confidence 367788999999864
No 177
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.55 E-value=24 Score=31.81 Aligned_cols=29 Identities=21% Similarity=0.371 Sum_probs=18.7
Q ss_pred ceeeCCCCCccchhhhhhccccccCCCCCCccccCCcc
Q 027446 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCA 80 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa 80 (223)
.--+||-|+-.+....+ .......||.|-
T Consensus 243 ~g~pCprCG~~I~~~~~---------~gR~t~~CP~CQ 271 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVV---------AGRSSHYCPHCQ 271 (272)
T ss_pred CCCcCCCCCCeeEEEEE---------CCCccEECcCCc
Confidence 34599999977643322 134567899994
No 178
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=29.34 E-value=9.1 Score=26.11 Aligned_cols=34 Identities=26% Similarity=0.662 Sum_probs=12.6
Q ss_pred eeCCCCCccchhhh---hhccccccCCCCCCc----------cccCCccC
Q 027446 45 FLCPFCAEDFDIVG---LCCHIDEDHPIEAKN----------GVCPVCAK 81 (223)
Q Consensus 45 F~CPfC~~~~d~~~---L~~H~~~eH~~e~k~----------~VCPVCa~ 81 (223)
..||+.+..+.+.+ .|.|++ +||..+ --||||.+
T Consensus 3 L~CPls~~~i~~P~Rg~~C~H~~---CFDl~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNCKHLQ---CFDLESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SB-TTTSSB-SSEEEETT--SS-----EEHHHHHHHHHHS---B-TTT--
T ss_pred eeCCCCCCEEEeCccCCcCcccc---eECHHHHHHHhhccCCeECcCCcC
Confidence 35666666555443 344432 444322 35888864
No 179
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=29.11 E-value=24 Score=19.72 Aligned_cols=15 Identities=27% Similarity=0.813 Sum_probs=6.9
Q ss_pred cCCccCccc--hhhhhh
Q 027446 76 CPVCAKRVG--TDIVSH 90 (223)
Q Consensus 76 CPVCa~~v~--~d~i~H 90 (223)
|.||..... ..+..|
T Consensus 3 C~~C~~~f~s~~~~~~H 19 (25)
T PF12874_consen 3 CDICNKSFSSENSLRQH 19 (25)
T ss_dssp ETTTTEEESSHHHHHHH
T ss_pred CCCCCCCcCCHHHHHHH
Confidence 555544433 244444
No 180
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=28.52 E-value=22 Score=33.20 Aligned_cols=18 Identities=28% Similarity=0.617 Sum_probs=14.7
Q ss_pred CccccCCccCccchhhhh
Q 027446 72 KNGVCPVCAKRVGTDIVS 89 (223)
Q Consensus 72 k~~VCPVCa~~v~~d~i~ 89 (223)
+..+||||..+|-..||.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 346999999999887774
No 181
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=28.09 E-value=32 Score=34.58 Aligned_cols=22 Identities=32% Similarity=0.537 Sum_probs=17.0
Q ss_pred ccccCCCCCCccccCCccCccc
Q 027446 63 IDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 63 ~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
|..+.-.+++.-|||||...||
T Consensus 83 c~~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 83 CPYNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred CCcccCCCCccCcCccccCCCC
Confidence 3344455788899999999988
No 182
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.31 E-value=41 Score=37.16 Aligned_cols=37 Identities=30% Similarity=0.541 Sum_probs=20.9
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
.+.||-|+...- ...|..|-. |. ++ ...||.|.+.+.
T Consensus 667 ~rkCPkCG~~t~-~~fCP~CGs-~t-e~-vy~CPsCGaev~ 703 (1337)
T PRK14714 667 RRRCPSCGTETY-ENRCPDCGT-HT-EP-VYVCPDCGAEVP 703 (1337)
T ss_pred EEECCCCCCccc-cccCcccCC-cC-CC-ceeCccCCCccC
Confidence 588888888621 236665653 21 11 236777766543
No 183
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.93 E-value=30 Score=25.20 Aligned_cols=13 Identities=38% Similarity=0.974 Sum_probs=9.2
Q ss_pred CCCccccCCccCc
Q 027446 70 EAKNGVCPVCAKR 82 (223)
Q Consensus 70 e~k~~VCPVCa~~ 82 (223)
+...++||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 5667778888765
No 184
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=26.78 E-value=36 Score=24.23 Aligned_cols=42 Identities=24% Similarity=0.412 Sum_probs=32.3
Q ss_pred ceeeCCCCCcc--chhhhhhccccccCCCCCCc-cccCCccCccc
Q 027446 43 AMFLCPFCAED--FDIVGLCCHIDEDHPIEAKN-GVCPVCAKRVG 84 (223)
Q Consensus 43 ~~F~CPfC~~~--~d~~~L~~H~~~eH~~e~k~-~VCPVCa~~v~ 84 (223)
...+|=||++. .....=|-|+.=.++++... --||+|-.++.
T Consensus 6 ~~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 6 PEQPCVFCGFVGTKGTVLPCGHLICDNCFPGERYNGCPFCGTPFE 50 (55)
T ss_pred cceeEEEccccccccccccccceeeccccChhhccCCCCCCCccc
Confidence 35678888875 77777899999888887654 47999988754
No 185
>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=26.77 E-value=8.5 Score=24.13 Aligned_cols=8 Identities=38% Similarity=1.132 Sum_probs=4.2
Q ss_pred CccccCCc
Q 027446 72 KNGVCPVC 79 (223)
Q Consensus 72 k~~VCPVC 79 (223)
....||+|
T Consensus 34 ~~~~CP~C 41 (41)
T PF00097_consen 34 GSVKCPLC 41 (41)
T ss_dssp SSSBTTTT
T ss_pred CCccCCcC
Confidence 34456665
No 186
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=26.63 E-value=20 Score=35.34 Aligned_cols=29 Identities=28% Similarity=0.590 Sum_probs=23.4
Q ss_pred CccccCCccCccc--hhhhhhhhhcccchhh
Q 027446 72 KNGVCPVCAKRVG--TDIVSHITMQHGNFFK 100 (223)
Q Consensus 72 k~~VCPVCa~~v~--~d~i~Hi~~qH~~~fk 100 (223)
+.-+||+|..+.. .++..|+-..|-..++
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 3457999998754 6899999999988774
No 187
>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=26.55 E-value=48 Score=26.30 Aligned_cols=34 Identities=26% Similarity=0.689 Sum_probs=24.5
Q ss_pred CccceeeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccchh
Q 027446 40 DLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTD 86 (223)
Q Consensus 40 d~~~~F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d 86 (223)
++.....||-||.. ||+. ..++|||-|..-+-..
T Consensus 5 elGtKR~Cp~CG~kFYDLn-------------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDLN-------------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCcccCCCCcchhccCC-------------CCCccCCCCCCccCcc
Confidence 45567789999986 6642 3468999998876544
No 188
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.26 E-value=39 Score=33.18 Aligned_cols=36 Identities=28% Similarity=0.649 Sum_probs=21.3
Q ss_pred eeeCCCCCccch----hhhhhcc-ccccCCCCCCccccCCccCc
Q 027446 44 MFLCPFCAEDFD----IVGLCCH-IDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 44 ~F~CPfC~~~~d----~~~L~~H-~~~eH~~e~k~~VCPVCa~~ 82 (223)
...||.|+..+. ...|.|| |.-. ..-+-.||.|...
T Consensus 222 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~---~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEGKLRCHYCGYQ---EPIPKTCPQCGSE 262 (505)
T ss_pred ccCCCCCCCceEEecCCCeEEcCCCcCc---CCCCCCCCCCCCC
Confidence 356999987532 3345454 3321 2234689999874
No 189
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.21 E-value=42 Score=34.37 Aligned_cols=39 Identities=18% Similarity=0.390 Sum_probs=25.7
Q ss_pred CccceeeCCCCCccchh----hhh-hccccccCCCCCCccccCCccCc
Q 027446 40 DLNAMFLCPFCAEDFDI----VGL-CCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d~----~~L-~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
+....+.||.|+-.+.. ..| |.||-- + ...-.||-|...
T Consensus 388 ~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~-~---~~p~~Cp~Cgs~ 431 (665)
T PRK14873 388 RCRTPARCRHCTGPLGLPSAGGTPRCRWCGR-A---APDWRCPRCGSD 431 (665)
T ss_pred hCcCeeECCCCCCceeEecCCCeeECCCCcC-C---CcCccCCCCcCC
Confidence 45567999999986433 246 555553 2 236699999875
No 190
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=26.13 E-value=34 Score=23.96 Aligned_cols=15 Identities=20% Similarity=0.510 Sum_probs=6.6
Q ss_pred ccceeeCCCCCccch
Q 027446 41 LNAMFLCPFCAEDFD 55 (223)
Q Consensus 41 ~~~~F~CPfC~~~~d 55 (223)
....+.||.....|.
T Consensus 8 ~~~~~~CPiT~~~~~ 22 (57)
T PF11789_consen 8 GTISLKCPITLQPFE 22 (57)
T ss_dssp SB--SB-TTTSSB-S
T ss_pred cEeccCCCCcCChhh
Confidence 445677776665543
No 191
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.11 E-value=43 Score=34.27 Aligned_cols=39 Identities=23% Similarity=0.612 Sum_probs=27.6
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccch
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
.-.||.||..+.. .-|.+|-.+-+.+++ .||-|-.+++.
T Consensus 15 akFC~~CG~~l~~-~~Cp~CG~~~~~~~~--fC~~CG~~~~~ 53 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQCGTEVPVDEA--HCPNCGAETGT 53 (645)
T ss_pred CccccccCCCCCC-CcCCCCCCCCCcccc--cccccCCcccc
Confidence 3468888887753 357788776554444 89999998664
No 192
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.10 E-value=29 Score=33.01 Aligned_cols=40 Identities=23% Similarity=0.535 Sum_probs=29.2
Q ss_pred eeCCCCCccchhhhhhccccccCCCCC---------CccccCCccCccc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEA---------KNGVCPVCAKRVG 84 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~---------k~~VCPVCa~~v~ 84 (223)
+.|-.|-++|..-..+.++-=.|.|-. +.-.||||--.+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~ 278 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIR 278 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCC
Confidence 999999999887777666666666622 3357999987554
No 193
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=25.85 E-value=22 Score=27.21 Aligned_cols=14 Identities=29% Similarity=0.672 Sum_probs=9.6
Q ss_pred eeCCCCCccchhhhh
Q 027446 45 FLCPFCAEDFDIVGL 59 (223)
Q Consensus 45 F~CPfC~~~~d~~~L 59 (223)
.+||+||. =|..+.
T Consensus 2 I~CP~CG~-R~~~EF 15 (84)
T PF04267_consen 2 IPCPHCGP-RDESEF 15 (84)
T ss_dssp EEETTTEE-EEGGGS
T ss_pred ccCCCCCc-cchhhe
Confidence 47999998 444444
No 194
>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=25.59 E-value=34 Score=22.62 Aligned_cols=11 Identities=36% Similarity=1.096 Sum_probs=8.4
Q ss_pred ceeeCCCCCcc
Q 027446 43 AMFLCPFCAED 53 (223)
Q Consensus 43 ~~F~CPfC~~~ 53 (223)
..|.||+|+..
T Consensus 17 ~g~~CP~Cg~~ 27 (46)
T PF12760_consen 17 DGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCe
Confidence 45889999864
No 195
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=25.58 E-value=41 Score=28.90 Aligned_cols=39 Identities=21% Similarity=0.322 Sum_probs=21.8
Q ss_pred eCCCCCccchh---hhhhccccccCCCCC-CccccCCccCccc
Q 027446 46 LCPFCAEDFDI---VGLCCHIDEDHPIEA-KNGVCPVCAKRVG 84 (223)
Q Consensus 46 ~CPfC~~~~d~---~~L~~H~~~eH~~e~-k~~VCPVCa~~v~ 84 (223)
.||+|+..+-- .+.-.-+.+.|.-.. ...+||.|-..-|
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 69999987332 222222222222222 2357999999866
No 196
>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=25.15 E-value=39 Score=33.32 Aligned_cols=15 Identities=40% Similarity=0.871 Sum_probs=13.6
Q ss_pred CCCccccCCccCccc
Q 027446 70 EAKNGVCPVCAKRVG 84 (223)
Q Consensus 70 e~k~~VCPVCa~~v~ 84 (223)
+++.-|||||...||
T Consensus 34 ~PNt~v~pvclg~PG 48 (478)
T TIGR00133 34 PPNTNVCPVCLGLPG 48 (478)
T ss_pred CCCcccCccccCCCC
Confidence 678899999999988
No 197
>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=24.61 E-value=36 Score=24.40 Aligned_cols=11 Identities=27% Similarity=0.833 Sum_probs=8.2
Q ss_pred eCCCCCccchh
Q 027446 46 LCPFCAEDFDI 56 (223)
Q Consensus 46 ~CPfC~~~~d~ 56 (223)
-||+||+.++.
T Consensus 5 HC~~CG~~Ip~ 15 (59)
T PF09889_consen 5 HCPVCGKPIPP 15 (59)
T ss_pred cCCcCCCcCCc
Confidence 58888887654
No 198
>PRK10445 endonuclease VIII; Provisional
Probab=24.50 E-value=35 Score=30.66 Aligned_cols=27 Identities=22% Similarity=0.362 Sum_probs=15.3
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCcc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCA 80 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa 80 (223)
-+||-|+..+..... .......||.|-
T Consensus 236 ~~Cp~Cg~~I~~~~~---------~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTL---------SSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEE---------CCCCcEECCCCc
Confidence 468888766443322 124456788773
No 199
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.45 E-value=42 Score=31.73 Aligned_cols=25 Identities=24% Similarity=0.483 Sum_probs=20.7
Q ss_pred CCCccceeeCCCCCccchhhhhhcc
Q 027446 38 DDDLNAMFLCPFCAEDFDIVGLCCH 62 (223)
Q Consensus 38 d~d~~~~F~CPfC~~~~d~~~L~~H 62 (223)
-+-+...|+||.|+..|-..+|..|
T Consensus 14 ~~q~~~~fpc~ic~r~f~~~~L~kh 38 (351)
T KOG3940|consen 14 LAQMQMRFPCRICQREFRRRELMKH 38 (351)
T ss_pred cccccccccccccccchhhhhhhcc
Confidence 3456779999999988888888877
No 200
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.40 E-value=30 Score=26.87 Aligned_cols=15 Identities=33% Similarity=0.899 Sum_probs=12.7
Q ss_pred CCccceeeCCCCCcc
Q 027446 39 DDLNAMFLCPFCAED 53 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~ 53 (223)
..+++.+.||+|+..
T Consensus 30 ~~~~~~~~Cp~C~~~ 44 (89)
T COG1997 30 AQQRAKHVCPFCGRT 44 (89)
T ss_pred HHHhcCCcCCCCCCc
Confidence 467889999999986
No 201
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=24.25 E-value=56 Score=20.55 Aligned_cols=11 Identities=18% Similarity=0.951 Sum_probs=6.4
Q ss_pred eeCCCCCccch
Q 027446 45 FLCPFCAEDFD 55 (223)
Q Consensus 45 F~CPfC~~~~d 55 (223)
|.|.-|+.+++
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 45666776655
No 202
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=23.93 E-value=35 Score=25.37 Aligned_cols=9 Identities=44% Similarity=1.390 Sum_probs=6.6
Q ss_pred eeCCCCCcc
Q 027446 45 FLCPFCAED 53 (223)
Q Consensus 45 F~CPfC~~~ 53 (223)
|.||+|+..
T Consensus 2 m~CP~Cg~~ 10 (72)
T PRK09678 2 FHCPLCQHA 10 (72)
T ss_pred ccCCCCCCc
Confidence 578888764
No 203
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=23.83 E-value=35 Score=30.65 Aligned_cols=28 Identities=21% Similarity=0.425 Sum_probs=17.7
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccC
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~ 81 (223)
-+||-|+..+....+ .......||.|-.
T Consensus 246 ~pC~~Cg~~I~~~~~---------~gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCRRCGTPIEKIKQ---------GGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCeeEEEEE---------CCCCcEECcCCCC
Confidence 479999977543222 1245568999954
No 204
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.82 E-value=28 Score=33.02 Aligned_cols=22 Identities=32% Similarity=0.920 Sum_probs=18.9
Q ss_pred eeeCCCCCccchhhhhhccccc
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDE 65 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~ 65 (223)
+.-||||.--+.....|.|++.
T Consensus 2 e~iCP~CkLsv~~~~m~~Hiea 23 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIEA 23 (393)
T ss_pred cccccceecccCHHHHHHHHHh
Confidence 3479999988999999999983
No 205
>PF04641 Rtf2: Rtf2 RING-finger
Probab=23.61 E-value=26 Score=31.29 Aligned_cols=45 Identities=31% Similarity=0.735 Sum_probs=27.7
Q ss_pred CccceeeCCCCCccch----hhhh--hccccccCCC-CCC-ccccCCccCccc
Q 027446 40 DLNAMFLCPFCAEDFD----IVGL--CCHIDEDHPI-EAK-NGVCPVCAKRVG 84 (223)
Q Consensus 40 d~~~~F~CPfC~~~~d----~~~L--~~H~~~eH~~-e~k-~~VCPVCa~~v~ 84 (223)
.....|.||.++.+|. .+.| |=|+..+-.. +.+ ...||+|.....
T Consensus 109 ~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 109 NSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFT 161 (260)
T ss_pred cCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhcccccccccCCccc
Confidence 4567899999998763 3333 2233322222 223 568999999844
No 206
>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=23.56 E-value=38 Score=24.16 Aligned_cols=10 Identities=40% Similarity=1.085 Sum_probs=8.6
Q ss_pred eeeCCCCCcc
Q 027446 44 MFLCPFCAED 53 (223)
Q Consensus 44 ~F~CPfC~~~ 53 (223)
..+||||+..
T Consensus 35 ~~pC~fCg~~ 44 (57)
T PF06221_consen 35 LGPCPFCGTP 44 (57)
T ss_pred cCcCCCCCCc
Confidence 5699999986
No 207
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.40 E-value=37 Score=30.76 Aligned_cols=27 Identities=22% Similarity=0.529 Sum_probs=17.2
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCcc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCA 80 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa 80 (223)
-+||-|+..+....+ .......||.|-
T Consensus 255 ~pC~~Cg~~I~~~~~---------~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKL---------AGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEE---------CCCccEECCCCc
Confidence 389999977543322 224556899984
No 208
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=22.86 E-value=28 Score=20.87 Aligned_cols=9 Identities=33% Similarity=0.770 Sum_probs=3.3
Q ss_pred eCCCCCccc
Q 027446 46 LCPFCAEDF 54 (223)
Q Consensus 46 ~CPfC~~~~ 54 (223)
+||=|+..+
T Consensus 3 ~C~rC~~~~ 11 (30)
T PF06827_consen 3 KCPRCWNYI 11 (30)
T ss_dssp B-TTT--BB
T ss_pred cCccCCCcc
Confidence 566666543
No 209
>cd03021 DsbA_GSTK DsbA family, Glutathione (GSH) S-transferase Kappa (GSTK) subfamily; GSTK is a member of the GST family of enzymes which catalyzes the transfer of the thiol of GSH to electrophilic substrates. It is specifically located in the mitochondria and peroxisomes, unlike other members of the canonical GST family, which are mainly cytosolic. The biological substrates of GSTK are not yet known. It is presumed to have a protective role during respiration when large amounts of reactive oxygen species are generated. GSTK has the same general fold as DsbA, consisting of a thioredoxin domain interrupted by an alpha-helical domain and its biological unit is a homodimer. GSTK is closely related to the bacterial enzyme, 2-hydroxychromene-2-carboxylate (HCCA) isomerase. It shows little sequence similarity to the other members of the GST family.
Probab=22.80 E-value=17 Score=30.81 Aligned_cols=13 Identities=15% Similarity=0.179 Sum_probs=10.4
Q ss_pred ccceeeCCCCCcc
Q 027446 41 LNAMFLCPFCAED 53 (223)
Q Consensus 41 ~~~~F~CPfC~~~ 53 (223)
....|.||||+.-
T Consensus 5 ~~~D~vcPwcylg 17 (209)
T cd03021 5 LYYDVVSPYSYLA 17 (209)
T ss_pred EEEeCCChHHHHH
Confidence 4567899999974
No 210
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=22.34 E-value=30 Score=36.68 Aligned_cols=52 Identities=25% Similarity=0.468 Sum_probs=38.6
Q ss_pred eeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccc--hhhhhhhhhcccchh
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG--TDIVSHITMQHGNFF 99 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~--~d~i~Hi~~qH~~~f 99 (223)
-+|-||++- =-.+.|.-|+.. |.. .+.-+|-||..+.. .|+--|+ ..|+..|
T Consensus 354 hkCr~CakvfgS~SaLqiHlRS-HTG-ERPfqCnvCG~~FSTkGNLKvH~-~rH~e~~ 408 (958)
T KOG1074|consen 354 HKCRFCAKVFGSDSALQIHLRS-HTG-ERPFQCNVCGNRFSTKGNLKVHF-QRHREKY 408 (958)
T ss_pred chhhhhHhhcCchhhhhhhhhc-cCC-CCCeeecccccccccccceeeee-eeccccC
Confidence 459999997 456789999884 655 46789999999976 5787786 3444444
No 211
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.11 E-value=41 Score=30.30 Aligned_cols=26 Identities=19% Similarity=0.534 Sum_probs=16.6
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVC 79 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVC 79 (223)
-+||-|+..+....+- ......||.|
T Consensus 246 ~pC~~Cg~~I~~~~~~---------gR~t~~CP~C 271 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVG---------GRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCeeEEEEEC---------CCCCEECCCC
Confidence 3888888775443331 2445678888
No 212
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=22.01 E-value=24 Score=36.44 Aligned_cols=47 Identities=21% Similarity=0.646 Sum_probs=32.6
Q ss_pred CccceeeCCCCCccc-hh-hhhhccccccC----CCCCCccccCCccCccchh
Q 027446 40 DLNAMFLCPFCAEDF-DI-VGLCCHIDEDH----PIEAKNGVCPVCAKRVGTD 86 (223)
Q Consensus 40 d~~~~F~CPfC~~~~-d~-~~L~~H~~~eH----~~e~k~~VCPVCa~~v~~d 86 (223)
+.+...+||.|.... |. -..|=|+-=+- +++++.--||.|....|.+
T Consensus 639 ~yK~~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan 691 (698)
T KOG0978|consen 639 EYKELLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN 691 (698)
T ss_pred HHHhceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence 357789999999763 33 23455554333 3477777899999999864
No 213
>PHA02776 E7 protein; Provisional
Probab=21.95 E-value=25 Score=27.86 Aligned_cols=38 Identities=29% Similarity=0.574 Sum_probs=24.3
Q ss_pred eeCCCCCccchhhhhhccccccC----CCCCCccccCCccCc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDH----PIEAKNGVCPVCAKR 82 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH----~~e~k~~VCPVCa~~ 82 (223)
-.|..|+..+.+..++.|-.-.. =.+.-..|||.|+.+
T Consensus 59 t~C~~C~~~lRL~V~st~~~IR~lqqLLl~~L~ivCp~Ca~~ 100 (101)
T PHA02776 59 TCCCGCDNNVRLVVECTEPDIQELHNLLLGSLNIVCPICAPK 100 (101)
T ss_pred eECCCCCCeEEEEEEcChhhHHHHHHHhcCCeEEECCCCCCC
Confidence 46888988777766665532110 124556789999875
No 214
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=21.89 E-value=51 Score=21.23 Aligned_cols=9 Identities=33% Similarity=0.837 Sum_probs=5.8
Q ss_pred eeeCCCCCc
Q 027446 44 MFLCPFCAE 52 (223)
Q Consensus 44 ~F~CPfC~~ 52 (223)
+..||+|+.
T Consensus 5 ~v~CP~C~s 13 (36)
T PF03811_consen 5 DVHCPRCQS 13 (36)
T ss_pred eeeCCCCCC
Confidence 456777765
No 215
>PHA00626 hypothetical protein
Probab=21.88 E-value=56 Score=23.54 Aligned_cols=17 Identities=24% Similarity=0.344 Sum_probs=11.1
Q ss_pred cccCCccCccchhhhhh
Q 027446 74 GVCPVCAKRVGTDIVSH 90 (223)
Q Consensus 74 ~VCPVCa~~v~~d~i~H 90 (223)
.+||.|-.+.++|..+.
T Consensus 24 YkCkdCGY~ft~~~~~~ 40 (59)
T PHA00626 24 YVCCDCGYNDSKDAFGE 40 (59)
T ss_pred eEcCCCCCeechhhhhh
Confidence 46777777776666554
No 216
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=21.83 E-value=30 Score=34.24 Aligned_cols=16 Identities=31% Similarity=0.686 Sum_probs=12.2
Q ss_pred ceeeCCCCCccchhhh
Q 027446 43 AMFLCPFCAEDFDIVG 58 (223)
Q Consensus 43 ~~F~CPfC~~~~d~~~ 58 (223)
..=+||.|=|.+|.+.
T Consensus 174 ELPTCpVCLERMD~s~ 189 (493)
T KOG0804|consen 174 ELPTCPVCLERMDSST 189 (493)
T ss_pred cCCCcchhHhhcCccc
Confidence 3458999999877665
No 217
>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=21.77 E-value=57 Score=21.64 Aligned_cols=23 Identities=22% Similarity=0.470 Sum_probs=14.1
Q ss_pred eCCCCCccchhhhhhccccccCCCCCCccccCCcc
Q 027446 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCA 80 (223)
Q Consensus 46 ~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa 80 (223)
.||-|+..+-. .-.+..+||+|.
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 79999765321 113357899983
No 218
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=21.70 E-value=51 Score=26.68 Aligned_cols=31 Identities=23% Similarity=0.559 Sum_probs=21.3
Q ss_pred CCccceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 39 DDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 39 ~d~~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
++.+..+.|.-|+..+....+ .+.||.|...
T Consensus 65 e~~p~~~~C~~C~~~~~~e~~-------------~~~CP~C~s~ 95 (115)
T COG0375 65 EEEPAECWCLDCGQEVELEEL-------------DYRCPKCGSI 95 (115)
T ss_pred EEeccEEEeccCCCeecchhh-------------eeECCCCCCC
Confidence 367889999999666543332 2349999853
No 219
>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=21.69 E-value=39 Score=25.91 Aligned_cols=14 Identities=21% Similarity=0.641 Sum_probs=8.9
Q ss_pred eeCCCCCccchhhhh
Q 027446 45 FLCPFCAEDFDIVGL 59 (223)
Q Consensus 45 F~CPfC~~~~d~~~L 59 (223)
.+||+|| .=|..+.
T Consensus 2 I~CP~CG-~R~~~EF 15 (84)
T TIGR01374 2 IPCPYCG-PRPEEEF 15 (84)
T ss_pred ccCCCCC-CccHhhE
Confidence 4799999 4444444
No 220
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=21.60 E-value=40 Score=29.29 Aligned_cols=14 Identities=36% Similarity=0.797 Sum_probs=11.6
Q ss_pred eeCCCCCccchhhh
Q 027446 45 FLCPFCAEDFDIVG 58 (223)
Q Consensus 45 F~CPfC~~~~d~~~ 58 (223)
=+||+|+..+|-.+
T Consensus 157 P~CPlCg~PldP~G 170 (177)
T TIGR03847 157 PPCPLCGRPIDPDG 170 (177)
T ss_pred CCCCCCCCCCCCCC
Confidence 57999999988654
No 221
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=21.57 E-value=35 Score=29.50 Aligned_cols=28 Identities=21% Similarity=0.615 Sum_probs=18.5
Q ss_pred eeeCCCCCccchhhhhhccccccCCCCCCccccCCccCccchhh
Q 027446 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDI 87 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~ 87 (223)
.-.||-||-. - ...+.|+-|..+|-...
T Consensus 93 l~~CP~CGh~----------k------~a~~LC~~Cy~kV~ket 120 (176)
T KOG4080|consen 93 LNTCPACGHI----------K------PAHTLCDYCYAKVHKET 120 (176)
T ss_pred cccCcccCcc----------c------cccccHHHHHHHHHHHH
Confidence 4589999842 2 23568888888775433
No 222
>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=21.50 E-value=31 Score=27.46 Aligned_cols=11 Identities=27% Similarity=0.658 Sum_probs=9.1
Q ss_pred ceeeCCCCCcc
Q 027446 43 AMFLCPFCAED 53 (223)
Q Consensus 43 ~~F~CPfC~~~ 53 (223)
..|.||+|..-
T Consensus 23 ~D~~Cp~C~~~ 33 (178)
T cd03019 23 FSYGCPHCYNF 33 (178)
T ss_pred ECCCCcchhhh
Confidence 46999999875
No 223
>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=21.48 E-value=24 Score=24.43 Aligned_cols=10 Identities=40% Similarity=0.780 Sum_probs=8.2
Q ss_pred eeeCCCCCcc
Q 027446 44 MFLCPFCAED 53 (223)
Q Consensus 44 ~F~CPfC~~~ 53 (223)
.+.||+|..-
T Consensus 6 d~~Cp~C~~~ 15 (98)
T cd02972 6 DPLCPYCYLF 15 (98)
T ss_pred CCCCHhHHhh
Confidence 5789999875
No 224
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=21.42 E-value=38 Score=31.46 Aligned_cols=43 Identities=19% Similarity=0.463 Sum_probs=31.0
Q ss_pred cceeeCCCCCccchhhhhhcc---ccccCCCCCCccccCCccCccc
Q 027446 42 NAMFLCPFCAEDFDIVGLCCH---IDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~~~L~~H---~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
-..+.||-|...+......++ +.=.=+-.....-||.|+..+|
T Consensus 46 ~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 46 LDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIG 91 (299)
T ss_pred hhhccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccc
Confidence 346899999999888888774 3332333345568999999887
No 225
>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=21.41 E-value=23 Score=29.04 Aligned_cols=20 Identities=15% Similarity=0.333 Sum_probs=12.9
Q ss_pred cceeeCCCCCcc-chhhhhhc
Q 027446 42 NAMFLCPFCAED-FDIVGLCC 61 (223)
Q Consensus 42 ~~~F~CPfC~~~-~d~~~L~~ 61 (223)
-..|.||||+.- -.+..+..
T Consensus 4 ~~D~~cP~cyl~~~~l~~~~~ 24 (201)
T cd03024 4 WSDVVCPWCYIGKRRLEKALA 24 (201)
T ss_pred EecCcCccHHHHHHHHHHHHH
Confidence 457899999964 34444443
No 226
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=21.27 E-value=32 Score=36.50 Aligned_cols=10 Identities=30% Similarity=0.820 Sum_probs=0.0
Q ss_pred eeeCCCCCcc
Q 027446 44 MFLCPFCAED 53 (223)
Q Consensus 44 ~F~CPfC~~~ 53 (223)
.+.||-|+..
T Consensus 655 ~r~Cp~Cg~~ 664 (900)
T PF03833_consen 655 RRRCPKCGKE 664 (900)
T ss_dssp ----------
T ss_pred cccCcccCCc
Confidence 4566666654
No 227
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.25 E-value=47 Score=29.94 Aligned_cols=31 Identities=19% Similarity=0.432 Sum_probs=20.7
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCccc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~ 84 (223)
-+||-|+..+....+ .......||.|-..++
T Consensus 236 ~pC~~Cg~~I~~~~~---------~gR~ty~Cp~CQ~~~~ 266 (269)
T PRK14811 236 QPCPRCGTPIEKIVV---------GGRGTHFCPQCQPLRP 266 (269)
T ss_pred CCCCcCCCeeEEEEE---------CCCCcEECCCCcCCCC
Confidence 389999987544333 1245678999987654
No 228
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.84 E-value=65 Score=22.36 Aligned_cols=31 Identities=23% Similarity=0.659 Sum_probs=20.6
Q ss_pred cceeeCCCCCccchhhhhhccccccCCCCCCccccCCccCcc
Q 027446 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (223)
Q Consensus 42 ~~~F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v 83 (223)
...|.|--|+..|+.. .....+.||-|..++
T Consensus 4 ~~~Y~C~~Cg~~~~~~-----------~~~~~irCp~Cg~rI 34 (49)
T COG1996 4 MMEYKCARCGREVELD-----------QETRGIRCPYCGSRI 34 (49)
T ss_pred eEEEEhhhcCCeeehh-----------hccCceeCCCCCcEE
Confidence 4578888898887321 123456799888764
No 229
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.67 E-value=45 Score=26.88 Aligned_cols=16 Identities=31% Similarity=0.617 Sum_probs=12.8
Q ss_pred eeeCCCCCccchhhhh
Q 027446 44 MFLCPFCAEDFDIVGL 59 (223)
Q Consensus 44 ~F~CPfC~~~~d~~~L 59 (223)
...||-||+.|+-+.+
T Consensus 49 ~t~CP~Cg~~~e~~fv 64 (115)
T COG1885 49 STSCPKCGEPFESAFV 64 (115)
T ss_pred cccCCCCCCccceeEE
Confidence 4589999999886654
No 230
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.45 E-value=56 Score=33.27 Aligned_cols=39 Identities=26% Similarity=0.501 Sum_probs=22.8
Q ss_pred cceeeCCCCCccch----hhhhhccccccCCCCCCccccCCccCc
Q 027446 42 NAMFLCPFCAEDFD----IVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 42 ~~~F~CPfC~~~~d----~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
...+.||.|+..+. ...|.||---. .....-.||.|...
T Consensus 388 g~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~--~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 388 GWVAECPHCDASLTLHRFQRRLRCHHCGY--QEPIPKACPECGST 430 (679)
T ss_pred cCccCCCCCCCceeEECCCCeEECCCCcC--CCCCCCCCCCCcCC
Confidence 34578999997632 34455553321 12234589999765
No 231
>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=20.41 E-value=21 Score=28.88 Aligned_cols=13 Identities=15% Similarity=0.202 Sum_probs=10.0
Q ss_pred ccceeeCCCCCcc
Q 027446 41 LNAMFLCPFCAED 53 (223)
Q Consensus 41 ~~~~F~CPfC~~~ 53 (223)
....|.||||+.-
T Consensus 3 ~~~D~~cP~cy~~ 15 (192)
T cd03022 3 FYFDFSSPYSYLA 15 (192)
T ss_pred EEEeCCChHHHHH
Confidence 3457899999974
No 232
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.25 E-value=70 Score=32.79 Aligned_cols=37 Identities=22% Similarity=0.610 Sum_probs=26.7
Q ss_pred eeCCCCCcc-chhhhhhccccccCCCCCCccccCCccCccch
Q 027446 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (223)
Q Consensus 45 F~CPfC~~~-~d~~~L~~H~~~eH~~e~k~~VCPVCa~~v~~ 85 (223)
..||-|+.+ -+-.-.|.+|-. +.. ..+||-|-+.+..
T Consensus 2 ~~Cp~Cg~~n~~~akFC~~CG~--~l~--~~~Cp~CG~~~~~ 39 (645)
T PRK14559 2 LICPQCQFENPNNNRFCQKCGT--SLT--HKPCPQCGTEVPV 39 (645)
T ss_pred CcCCCCCCcCCCCCccccccCC--CCC--CCcCCCCCCCCCc
Confidence 379999997 566777888853 332 2479999998653
No 233
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.24 E-value=38 Score=35.89 Aligned_cols=46 Identities=28% Similarity=0.554 Sum_probs=37.8
Q ss_pred eeCCCCCccchhh---hhhccccccCCCCCCccccCCccCcc--chhhhhh
Q 027446 45 FLCPFCAEDFDIV---GLCCHIDEDHPIEAKNGVCPVCAKRV--GTDIVSH 90 (223)
Q Consensus 45 F~CPfC~~~~d~~---~L~~H~~~eH~~e~k~~VCPVCa~~v--~~d~i~H 90 (223)
=+|--|+-.+|+. .+|-|.--.||++.+...||-|..-. +++|++.
T Consensus 841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~~~~m~l~~s 891 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPELRGVMDLKRS 891 (933)
T ss_pred eeecccCCccccceeeeecccHHHHHhhccCcccCCccchhhhhhHHHHHH
Confidence 3999999988865 58999999999999999999999832 3566653
No 234
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=20.19 E-value=51 Score=29.51 Aligned_cols=27 Identities=22% Similarity=0.619 Sum_probs=17.8
Q ss_pred eeCCCCCccchhhhhhccccccCCCCCCccccCCccCc
Q 027446 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (223)
Q Consensus 45 F~CPfC~~~~d~~~L~~H~~~eH~~e~k~~VCPVCa~~ 82 (223)
=.||+||..+... .+....+||.|...
T Consensus 100 ~fC~~CG~~~~~~-----------~~~~~~~C~~c~~~ 126 (256)
T PRK00241 100 RFCGYCGHPMHPS-----------KTEWAMLCPHCRER 126 (256)
T ss_pred ccccccCCCCeec-----------CCceeEECCCCCCE
Confidence 3799999975432 12334578888865
No 235
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=20.11 E-value=28 Score=31.17 Aligned_cols=47 Identities=21% Similarity=0.400 Sum_probs=29.4
Q ss_pred CccceeeCCCCCcc---chhh------hhhccccccCCCCCCccccCCccCccchhhhhhhh
Q 027446 40 DLNAMFLCPFCAED---FDIV------GLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHIT 92 (223)
Q Consensus 40 d~~~~F~CPfC~~~---~d~~------~L~~H~~~eH~~e~k~~VCPVCa~~v~~d~i~Hi~ 92 (223)
+..+.+.||+|+.- |+-. .+.-++. -||++..+..||- |.|...++.
T Consensus 9 ~v~sD~vCPwC~ig~~rL~ka~~~~~~~~~v~i~-w~pf~l~p~~~~~-----g~~~~~~l~ 64 (225)
T COG2761 9 DVFSDVVCPWCYIGKRRLEKALAEYPQEVRVEIR-WRPFELDPDLPPE-----GLDRKEYLA 64 (225)
T ss_pred EEEeCCcCchhhcCHHHHHHHHHhcCcceeEEEE-ecccccCCCCCcc-----cccHHHHHH
Confidence 56678999999863 3321 1122333 4788888888886 666666643
Done!