Query 029136
Match_columns 198
No_of_seqs 120 out of 142
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 08:04:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029136.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029136hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14571 Di19_C: Stress-induce 99.8 2.1E-20 4.6E-25 144.9 1.9 95 94-192 3-102 (105)
2 PF05605 zf-Di19: Drought indu 99.8 6.1E-20 1.3E-24 125.5 4.0 53 22-74 2-54 (54)
3 KOG1280 Uncharacterized conser 97.6 3.9E-05 8.5E-10 71.3 3.0 41 22-62 79-120 (381)
4 KOG2923 Uncharacterized conser 94.8 0.013 2.7E-07 43.3 1.2 46 10-62 9-55 (67)
5 COG5216 Uncharacterized conser 94.2 0.017 3.7E-07 42.3 0.6 38 18-62 18-55 (67)
6 PF13894 zf-C2H2_4: C2H2-type 92.0 0.12 2.6E-06 28.1 1.8 23 23-45 1-24 (24)
7 COG5236 Uncharacterized conser 91.9 0.24 5.1E-06 47.3 4.6 64 18-87 216-319 (493)
8 PHA00732 hypothetical protein 89.5 0.31 6.8E-06 36.2 2.5 42 23-69 2-44 (79)
9 PF13913 zf-C2HC_2: zinc-finge 89.3 0.26 5.6E-06 29.3 1.6 21 22-42 2-22 (25)
10 PLN03086 PRLI-interacting fact 89.1 0.36 7.9E-06 47.6 3.3 47 19-70 450-497 (567)
11 PF13909 zf-H2C2_5: C2H2-type 89.1 0.3 6.5E-06 27.8 1.7 24 23-46 1-24 (24)
12 KOG1842 FYVE finger-containing 88.8 0.23 4.9E-06 48.2 1.7 35 17-51 10-45 (505)
13 PF12756 zf-C2H2_2: C2H2 type 87.4 0.36 7.8E-06 34.2 1.6 48 24-71 1-72 (100)
14 PF00096 zf-C2H2: Zinc finger, 87.3 0.4 8.6E-06 26.7 1.4 21 23-43 1-22 (23)
15 PF09237 GAGA: GAGA factor; I 85.1 0.58 1.3E-05 33.4 1.7 27 48-74 21-49 (54)
16 smart00531 TFIIE Transcription 84.8 0.72 1.6E-05 37.2 2.3 40 18-62 95-134 (147)
17 smart00834 CxxC_CXXC_SSSS Puta 84.1 0.39 8.6E-06 30.1 0.4 32 21-60 4-35 (41)
18 TIGR02098 MJ0042_CXXC MJ0042 f 83.0 0.61 1.3E-05 29.3 1.0 32 23-60 3-34 (38)
19 TIGR02605 CxxC_CxxC_SSSS putat 78.9 1.3 2.7E-05 29.5 1.5 32 21-60 4-35 (52)
20 PLN03208 E3 ubiquitin-protein 78.2 0.93 2E-05 39.3 0.8 46 20-65 16-82 (193)
21 PF08996 zf-DNA_Pol: DNA Polym 78.2 0.74 1.6E-05 38.6 0.2 56 21-78 17-73 (188)
22 smart00504 Ubox Modified RING 77.8 2.3 5.1E-05 28.4 2.5 27 29-62 20-46 (63)
23 PF04780 DUF629: Protein of un 77.8 1.6 3.5E-05 42.3 2.4 44 20-63 55-102 (466)
24 PF08271 TF_Zn_Ribbon: TFIIB z 76.6 0.76 1.6E-05 30.0 -0.1 34 23-66 1-34 (43)
25 PRK09710 lar restriction allev 76.3 0.91 2E-05 33.3 0.2 32 22-62 6-38 (64)
26 PF12756 zf-C2H2_2: C2H2 type 75.9 1.9 4.2E-05 30.4 1.8 26 21-46 49-75 (100)
27 PF08274 PhnA_Zn_Ribbon: PhnA 74.7 1.1 2.3E-05 28.3 0.2 24 24-59 4-27 (30)
28 TIGR01206 lysW lysine biosynth 74.7 0.97 2.1E-05 31.8 -0.0 30 22-60 2-31 (54)
29 PHA00733 hypothetical protein 74.5 4.5 9.7E-05 32.3 3.7 48 22-73 73-123 (128)
30 PF09986 DUF2225: Uncharacteri 74.2 0.78 1.7E-05 39.4 -0.7 57 21-77 4-74 (214)
31 PLN03086 PRLI-interacting fact 72.4 3.5 7.7E-05 40.9 3.2 39 21-62 477-515 (567)
32 cd00350 rubredoxin_like Rubred 70.9 1.9 4.2E-05 26.9 0.7 25 23-60 2-26 (33)
33 PF14354 Lar_restr_allev: Rest 70.3 1.9 4.2E-05 29.3 0.7 30 23-59 4-37 (61)
34 PF14255 Cys_rich_CPXG: Cystei 70.2 1.5 3.2E-05 30.7 0.1 13 23-35 1-13 (52)
35 PRK00398 rpoP DNA-directed RNA 70.2 2.6 5.7E-05 27.7 1.3 29 22-61 3-31 (46)
36 PHA02768 hypothetical protein; 68.9 4.1 9E-05 28.9 2.1 34 22-59 5-39 (55)
37 PF03145 Sina: Seven in absent 66.7 3.7 8.1E-05 34.1 1.8 54 21-77 13-75 (198)
38 cd00729 rubredoxin_SM Rubredox 66.1 3 6.6E-05 26.4 0.9 26 22-60 2-27 (34)
39 COG5175 MOT2 Transcriptional r 65.4 4.1 8.9E-05 39.0 2.0 31 25-60 17-62 (480)
40 smart00734 ZnF_Rad18 Rad18-lik 64.5 5.2 0.00011 24.0 1.7 9 53-61 3-11 (26)
41 PF03470 zf-XS: XS zinc finger 63.5 4.5 9.8E-05 27.6 1.4 9 54-62 1-9 (43)
42 PF02176 zf-TRAF: TRAF-type zi 62.9 2.8 6E-05 28.1 0.3 45 22-68 9-60 (60)
43 COG4049 Uncharacterized protei 62.3 3.7 7.9E-05 30.1 0.8 27 52-78 18-46 (65)
44 TIGR03655 anti_R_Lar restricti 60.4 3.7 8.1E-05 27.9 0.6 8 53-60 28-35 (53)
45 PF05129 Elf1: Transcription e 60.1 3.4 7.5E-05 30.9 0.4 34 20-60 20-55 (81)
46 PRK12496 hypothetical protein; 59.5 5 0.00011 33.3 1.3 29 20-61 125-153 (164)
47 PF09723 Zn-ribbon_8: Zinc rib 59.5 4.6 0.0001 26.4 0.9 31 21-59 4-34 (42)
48 PF13465 zf-H2C2_2: Zinc-finge 59.0 3.6 7.8E-05 24.2 0.3 10 23-32 15-24 (26)
49 KOG2462 C2H2-type Zn-finger pr 56.7 8.2 0.00018 35.4 2.3 37 20-60 159-196 (279)
50 PF12773 DZR: Double zinc ribb 55.7 6.3 0.00014 25.8 1.0 27 24-62 14-40 (50)
51 PRK14890 putative Zn-ribbon RN 55.1 6.6 0.00014 28.5 1.1 32 20-58 23-55 (59)
52 PTZ00255 60S ribosomal protein 55.0 3.1 6.7E-05 32.3 -0.6 15 16-30 30-44 (90)
53 KOG2462 C2H2-type Zn-finger pr 54.8 10 0.00023 34.8 2.6 52 22-76 187-241 (279)
54 KOG3623 Homeobox transcription 54.6 7.8 0.00017 40.3 1.9 43 19-61 207-250 (1007)
55 PF05605 zf-Di19: Drought indu 53.7 9 0.00019 25.8 1.6 24 22-46 31-54 (54)
56 PF04423 Rad50_zn_hook: Rad50 53.7 8.9 0.00019 25.9 1.5 22 52-73 21-46 (54)
57 PF09538 FYDLN_acid: Protein o 53.3 6.9 0.00015 30.9 1.1 35 17-64 4-39 (108)
58 PF14206 Cys_rich_CPCC: Cystei 53.1 5.2 0.00011 30.1 0.4 26 22-58 1-27 (78)
59 TIGR00373 conserved hypothetic 53.1 11 0.00023 31.0 2.2 35 18-62 105-139 (158)
60 PRK06266 transcription initiat 52.7 11 0.00024 31.7 2.3 34 19-62 114-147 (178)
61 PF07282 OrfB_Zn_ribbon: Putat 52.6 10 0.00022 26.2 1.8 41 18-69 24-64 (69)
62 PF05207 zf-CSL: CSL zinc fing 52.4 5.1 0.00011 27.8 0.2 45 9-62 4-51 (55)
63 PF15616 TerY-C: TerY-C metal 51.5 4.4 9.6E-05 33.2 -0.3 46 18-65 73-119 (131)
64 PF04564 U-box: U-box domain; 51.1 20 0.00043 25.6 3.1 28 30-63 24-51 (73)
65 PF07754 DUF1610: Domain of un 50.9 8.1 0.00018 23.4 0.9 12 19-30 13-24 (24)
66 PHA00616 hypothetical protein 49.3 12 0.00025 25.6 1.6 25 23-47 2-27 (44)
67 TIGR00280 L37a ribosomal prote 49.0 4.3 9.4E-05 31.6 -0.7 15 16-30 29-43 (91)
68 PF13912 zf-C2H2_6: C2H2-type 48.5 13 0.00028 21.2 1.5 23 23-45 2-25 (27)
69 PF13395 HNH_4: HNH endonuclea 48.1 8.8 0.00019 26.1 0.8 14 25-38 1-14 (54)
70 PF02892 zf-BED: BED zinc fing 48.0 11 0.00024 24.0 1.3 25 21-45 15-44 (45)
71 PF08209 Sgf11: Sgf11 (transcr 47.0 11 0.00024 24.2 1.1 17 53-69 6-23 (33)
72 TIGR00100 hypA hydrogenase nic 46.8 7.5 0.00016 30.4 0.4 31 17-60 65-95 (115)
73 PRK03976 rpl37ae 50S ribosomal 46.3 4.9 0.00011 31.2 -0.7 14 17-30 31-44 (90)
74 smart00659 RPOLCX RNA polymera 46.0 11 0.00024 25.3 1.1 28 22-61 2-29 (44)
75 smart00355 ZnF_C2H2 zinc finge 45.5 18 0.00039 19.1 1.7 20 23-42 1-21 (26)
76 PF01155 HypA: Hydrogenase exp 43.8 8.3 0.00018 30.0 0.2 31 17-60 65-95 (113)
77 COG4888 Uncharacterized Zn rib 43.5 11 0.00024 30.1 0.8 37 19-60 19-55 (104)
78 cd03021 DsbA_GSTK DsbA family, 43.1 6.2 0.00013 32.6 -0.6 13 18-30 4-16 (209)
79 smart00507 HNHc HNH nucleases. 42.2 4.3 9.4E-05 25.1 -1.3 21 23-43 11-31 (52)
80 COG4311 SoxD Sarcosine oxidase 42.2 11 0.00024 29.8 0.7 9 22-30 3-11 (97)
81 KOG2231 Predicted E3 ubiquitin 42.0 17 0.00037 36.9 2.1 30 19-48 179-209 (669)
82 PF10058 DUF2296: Predicted in 41.7 17 0.00037 25.4 1.5 8 22-29 44-51 (54)
83 COG2888 Predicted Zn-ribbon RN 41.2 25 0.00053 25.8 2.3 34 18-58 23-57 (61)
84 TIGR00686 phnA alkylphosphonat 41.2 11 0.00023 30.4 0.4 25 24-60 4-28 (109)
85 COG0675 Transposase and inacti 40.6 20 0.00044 30.1 2.0 35 21-71 308-342 (364)
86 cd03024 DsbA_FrnE DsbA family, 40.2 8.5 0.00018 30.7 -0.3 24 18-41 2-26 (201)
87 PF11793 FANCL_C: FANCL C-term 39.5 20 0.00044 25.7 1.7 47 17-63 15-67 (70)
88 PF13248 zf-ribbon_3: zinc-rib 39.4 17 0.00037 21.5 1.0 10 23-32 3-12 (26)
89 PRK12495 hypothetical protein; 39.3 15 0.00032 32.9 1.0 30 21-63 41-70 (226)
90 PRK03922 hypothetical protein; 39.3 13 0.00028 30.1 0.6 14 22-35 49-62 (113)
91 KOG2177 Predicted E3 ubiquitin 39.0 14 0.00031 29.2 0.8 41 19-59 10-55 (386)
92 PF01780 Ribosomal_L37ae: Ribo 38.9 7.7 0.00017 30.1 -0.7 14 17-30 30-43 (90)
93 cd03022 DsbA_HCCA_Iso DsbA fam 38.6 8.3 0.00018 30.4 -0.6 37 157-195 144-180 (192)
94 KOG2593 Transcription initiati 38.4 27 0.00058 34.0 2.7 59 12-77 118-190 (436)
95 PRK00464 nrdR transcriptional 38.4 14 0.00031 30.7 0.8 32 24-61 2-38 (154)
96 PF04475 DUF555: Protein of un 38.2 14 0.0003 29.5 0.6 14 22-35 47-60 (102)
97 KOG0320 Predicted E3 ubiquitin 37.9 24 0.00052 30.8 2.1 41 21-63 130-179 (187)
98 PHA02929 N1R/p28-like protein; 37.8 6.4 0.00014 35.0 -1.4 43 20-62 172-227 (238)
99 PF04780 DUF629: Protein of un 37.2 18 0.0004 35.2 1.4 49 31-79 20-87 (466)
100 PRK12380 hydrogenase nickel in 36.8 14 0.00029 29.0 0.4 31 17-60 65-95 (113)
101 smart00614 ZnF_BED BED zinc fi 36.6 26 0.00056 23.3 1.7 26 21-46 17-48 (50)
102 PF06957 COPI_C: Coatomer (COP 36.6 18 0.0004 34.7 1.3 35 20-67 378-413 (422)
103 PF02146 SIR2: Sir2 family; I 36.5 21 0.00046 28.9 1.5 37 21-62 104-140 (178)
104 PF14616 DUF4451: Domain of un 36.4 19 0.0004 28.8 1.1 26 51-76 25-55 (124)
105 PF10571 UPF0547: Uncharacteri 36.0 21 0.00045 21.6 1.1 8 25-32 3-10 (26)
106 PF13824 zf-Mss51: Zinc-finger 35.3 11 0.00023 26.9 -0.3 10 20-29 12-21 (55)
107 PRK11595 DNA utilization prote 35.2 19 0.0004 30.8 1.0 35 24-60 7-43 (227)
108 PF00301 Rubredoxin: Rubredoxi 34.6 18 0.00039 24.7 0.7 12 18-29 30-41 (47)
109 PRK03824 hypA hydrogenase nick 34.4 19 0.00042 28.9 1.0 18 18-35 66-83 (135)
110 COG1499 NMD3 NMD protein affec 34.2 21 0.00045 33.6 1.2 40 21-60 5-52 (355)
111 PF13240 zinc_ribbon_2: zinc-r 34.0 12 0.00026 21.9 -0.2 6 25-30 2-7 (23)
112 TIGR02300 FYDLN_acid conserved 32.9 23 0.00049 29.3 1.1 32 18-62 5-37 (129)
113 TIGR00570 cdk7 CDK-activating 31.9 25 0.00053 32.7 1.3 39 23-62 4-54 (309)
114 PRK11088 rrmA 23S rRNA methylt 31.4 12 0.00025 32.3 -0.8 32 22-53 2-34 (272)
115 COG2761 FrnE Predicted dithiol 31.2 16 0.00034 32.5 -0.1 43 152-196 156-199 (225)
116 PRK00420 hypothetical protein; 30.8 30 0.00066 27.7 1.5 28 22-61 23-50 (112)
117 PRK04023 DNA polymerase II lar 30.3 22 0.00049 38.0 0.9 38 21-62 637-674 (1121)
118 COG3058 FdhE Uncharacterized p 30.3 17 0.00037 33.8 -0.0 19 50-68 184-202 (308)
119 PF14311 DUF4379: Domain of un 30.3 40 0.00087 22.7 1.9 39 11-57 17-55 (55)
120 PF01844 HNH: HNH endonuclease 30.2 6 0.00013 25.0 -2.2 11 25-35 1-11 (47)
121 PF05876 Terminase_GpA: Phage 29.9 23 0.00049 34.6 0.8 42 20-63 198-241 (557)
122 PF07191 zinc-ribbons_6: zinc- 29.9 6.2 0.00013 29.4 -2.4 55 24-82 3-64 (70)
123 PF13462 Thioredoxin_4: Thiore 29.7 12 0.00027 28.4 -0.8 22 20-41 19-41 (162)
124 PF11672 DUF3268: Protein of u 29.4 19 0.00042 28.3 0.2 37 24-63 4-43 (102)
125 PF03966 Trm112p: Trm112p-like 29.3 38 0.00083 23.8 1.7 37 22-59 7-61 (68)
126 PF14279 HNH_5: HNH endonuclea 29.3 26 0.00055 25.6 0.8 40 25-69 1-48 (71)
127 KOG4696 Uncharacterized conser 29.1 31 0.00066 32.8 1.4 23 22-45 2-24 (393)
128 cd03019 DsbA_DsbA DsbA family, 29.0 20 0.00043 27.8 0.2 17 173-189 134-150 (178)
129 cd00730 rubredoxin Rubredoxin; 28.9 31 0.00066 23.8 1.1 13 18-30 30-42 (50)
130 KOG2482 Predicted C2H2-type Zn 28.8 27 0.00059 33.6 1.0 30 22-51 279-309 (423)
131 TIGR00599 rad18 DNA repair pro 28.8 26 0.00057 33.4 1.0 44 17-62 21-71 (397)
132 KOG4173 Alpha-SNAP protein [In 28.8 40 0.00086 30.4 2.0 54 21-78 78-135 (253)
133 COG1675 TFA1 Transcription ini 28.4 41 0.00089 28.8 2.0 30 21-62 112-143 (176)
134 PRK10220 hypothetical protein; 28.2 30 0.00066 27.9 1.1 12 49-60 18-29 (111)
135 PRK14892 putative transcriptio 28.2 26 0.00057 27.4 0.7 36 20-63 19-54 (99)
136 cd02972 DsbA_family DsbA famil 28.0 17 0.00036 24.4 -0.4 10 21-30 5-14 (98)
137 PRK05477 gatB aspartyl/glutamy 27.4 25 0.00054 34.2 0.6 17 46-62 32-48 (474)
138 PF00097 zf-C3HC4: Zinc finger 27.1 9 0.00019 23.7 -1.7 9 49-57 33-41 (41)
139 COG1997 RPL43A Ribosomal prote 26.5 16 0.00034 28.5 -0.8 35 15-60 28-62 (89)
140 PF14353 CpXC: CpXC protein 26.5 31 0.00068 26.7 0.9 14 21-34 37-50 (128)
141 PF14828 Amnionless: Amnionles 25.5 32 0.0007 32.9 0.9 42 24-66 193-241 (437)
142 PF01323 DSBA: DSBA-like thior 25.5 12 0.00025 29.5 -1.7 20 19-38 4-24 (193)
143 KOG0402 60S ribosomal protein 25.2 21 0.00046 27.9 -0.3 11 20-30 34-44 (92)
144 PF13719 zinc_ribbon_5: zinc-r 25.2 41 0.0009 21.4 1.1 31 23-59 3-33 (37)
145 COG4391 Uncharacterized protei 24.9 33 0.00071 25.2 0.7 13 48-60 45-57 (62)
146 KOG1002 Nucleotide excision re 24.8 48 0.001 33.8 2.0 54 16-69 530-593 (791)
147 smart00451 ZnF_U1 U1-like zinc 23.8 58 0.0013 19.3 1.6 20 23-42 4-24 (35)
148 cd03023 DsbA_Com1_like DsbA fa 23.6 23 0.00051 26.3 -0.3 34 161-196 110-143 (154)
149 PF12013 DUF3505: Protein of u 23.1 56 0.0012 24.7 1.7 31 46-76 6-37 (109)
150 PF12660 zf-TFIIIC: Putative z 23.0 17 0.00037 27.9 -1.2 38 24-61 16-65 (99)
151 PF04267 SoxD: Sarcosine oxida 22.9 29 0.00063 26.6 0.1 8 23-30 2-9 (84)
152 PF10276 zf-CHCC: Zinc-finger 22.4 30 0.00065 23.0 0.1 10 22-31 29-38 (40)
153 PLN02751 glutamyl-tRNA(Gln) am 22.4 34 0.00074 34.0 0.5 20 43-62 85-104 (544)
154 COG5189 SFP1 Putative transcri 22.3 42 0.00092 32.1 1.1 41 21-61 348-408 (423)
155 PF02934 GatB_N: GatB/GatE cat 21.6 33 0.00072 31.5 0.2 20 44-63 25-44 (289)
156 PF10265 DUF2217: Uncharacteri 21.4 1.5E+02 0.0032 29.6 4.5 12 74-85 32-43 (514)
157 COG1592 Rubrerythrin [Energy p 21.2 42 0.00091 28.5 0.7 12 49-60 147-158 (166)
158 PRK00564 hypA hydrogenase nick 21.2 38 0.00082 26.6 0.4 32 17-60 66-97 (117)
159 PF14968 CCDC84: Coiled coil p 21.2 48 0.0011 31.1 1.2 20 16-35 52-71 (336)
160 TIGR00165 S18 ribosomal protei 21.0 53 0.0012 24.2 1.1 30 49-78 3-38 (70)
161 KOG2879 Predicted E3 ubiquitin 20.8 25 0.00054 32.6 -0.8 41 21-61 238-286 (298)
162 KOG1493 Anaphase-promoting com 20.7 74 0.0016 24.6 1.9 37 22-59 31-78 (84)
163 PF14570 zf-RING_4: RING/Ubox 20.7 45 0.00098 23.1 0.7 32 21-59 14-45 (48)
164 PF12230 PRP21_like_P: Pre-mRN 20.4 34 0.00073 29.2 0.0 20 52-71 169-189 (229)
165 KOG3940 Uncharacterized conser 20.3 57 0.0012 30.9 1.4 29 12-40 10-38 (351)
No 1
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=99.79 E-value=2.1e-20 Score=144.85 Aligned_cols=95 Identities=23% Similarity=0.318 Sum_probs=81.1
Q ss_pred hhhcch-----hhhccCCCCccCCCCCCCCCCCcchhhccCCCCCCCCCCccccccCcccccccccCCCCchhhHHhhhH
Q 029136 94 AMLGKE-----LSSFLGSPTIVRGNAPESLPDPLLSPFLCSGTLSDTKGIQKDDCTNKFSLASDLKRYPPSSEYKLLWSQ 168 (198)
Q Consensus 94 ~ll~k~-----Lqsllggs~~~~~~ssn~~pDPLLSsFi~~~~~~e~~~~e~s~~~~~~s~~~~~~r~~~~~~~k~~~~~ 168 (198)
.+|||| ||+||||+++++++++|++|||||||||||++.++ .++..+.......+...+.......|+.+.++
T Consensus 3 sll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~--~~~~~~~~~~~~~~~s~~~~~~~~~~~~s~~~ 80 (105)
T PF14571_consen 3 SLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPE--AEEPSKSSSSSEEKKSSKKSSSEQNVKSSADS 80 (105)
T ss_pred chhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCcc--ccccCCccccccccccccccchhcccccccCC
Confidence 367886 79999998667789999999999999999999998 66666654444445667778889999999999
Q ss_pred HHHHHHhcccccccchhhhhhhhe
Q 029136 169 LLFKKLANKISVSSTMHFKIDVLL 192 (198)
Q Consensus 169 ~l~~~~~~~~~~~~~~~~~~~~~~ 192 (198)
.|.+|++++...| ..|||.+||
T Consensus 81 ~lS~ee~eEk~~R--seFVQ~Lll 102 (105)
T PF14571_consen 81 SLSDEEQEEKAQR--SEFVQGLLL 102 (105)
T ss_pred CCCHHHHHHHHHH--HHHHHHHHH
Confidence 9999999999999 999999987
No 2
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=99.79 E-value=6.1e-20 Score=125.53 Aligned_cols=53 Identities=32% Similarity=0.726 Sum_probs=51.6
Q ss_pred eecCCCCccchhHHHHHhhhhhhccCCcccccccccccchhhhHhhhHhhhhh
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHFMVQHA 74 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~d~v~Hit~qH~ 74 (198)
+|+||||+++||+.+|+.|++++|+.+.+++|||||+.+++.||++||+.+||
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 69999999999999999999999999999999999999999999999999996
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=97.60 E-value=3.9e-05 Score=71.30 Aligned_cols=41 Identities=32% Similarity=0.747 Sum_probs=38.8
Q ss_pred eecCCCCcc-chhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 22 CFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 22 ~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
.|.||||++ .|....+.+|+..+|+.....++||||+..+.
T Consensus 79 SftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~ 120 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPE 120 (381)
T ss_pred cccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcc
Confidence 899999998 99999999999999999998899999999865
No 4
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.85 E-value=0.013 Score=43.26 Aligned_cols=46 Identities=22% Similarity=0.486 Sum_probs=28.8
Q ss_pred ccccc-cccCcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 10 VDETE-IDDDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 10 ~de~e-~ddd~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
|+|++ ++|.-..+|||| |+..|.+. .++=..--..+.||-|+-.+.
T Consensus 9 iedfe~~~e~~~y~yPCp-CGDrf~It------~edL~~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 9 IEDFEFDEENQTYYYPCP-CGDRFQIT------LEDLENGEDVARCPSCSLIIR 55 (67)
T ss_pred eecceeccCCCeEEcCCC-CCCeeeec------HHHHhCCCeeecCCCceEEEE
Confidence 45665 334456799999 98766554 111122334578999998764
No 5
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.22 E-value=0.017 Score=42.32 Aligned_cols=38 Identities=26% Similarity=0.501 Sum_probs=24.8
Q ss_pred CcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 18 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 18 d~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
+-..+|||| |+.-|.+. +++- ..--+.++||-|+-+|-
T Consensus 18 ~~~ftyPCP-CGDRFeIs-----LeDl-~~GE~VArCPSCSLiv~ 55 (67)
T COG5216 18 EKTFTYPCP-CGDRFEIS-----LEDL-RNGEVVARCPSCSLIVC 55 (67)
T ss_pred CceEEecCC-CCCEeEEE-----HHHh-hCCceEEEcCCceEEEE
Confidence 345799999 98766554 1111 22345688999998764
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=92.02 E-value=0.12 Score=28.11 Aligned_cols=23 Identities=26% Similarity=0.595 Sum_probs=15.1
Q ss_pred ecCCCCcc-chhHHHHHhhhhhhc
Q 029136 23 FPCPFCYL-EIEAHMICSHLQEEH 45 (198)
Q Consensus 23 F~CPfC~e-~fD~~~Lc~H~~eeH 45 (198)
|.||+|+. --+..+|-.|+...|
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 67888876 445677778877665
No 7
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=91.88 E-value=0.24 Score=47.25 Aligned_cols=64 Identities=19% Similarity=0.319 Sum_probs=47.5
Q ss_pred CcceeecCCCCcc-chhHHHHHhhhhhhccCCcccccccccccc-------------------------------hh---
Q 029136 18 DVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN-------------------------------LG--- 62 (198)
Q Consensus 18 d~r~~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~-------------------------------v~--- 62 (198)
-++--=.|-||.. =+|-.+|..||.+.|- .|-||..+ ++
T Consensus 216 GFKGHP~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~ 289 (493)
T COG5236 216 GFKGHPLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCY 289 (493)
T ss_pred CcCCCchhhhccceecChHHHHHHHHhhhh------hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEE
Confidence 3555668999976 7899999999999884 47777654 11
Q ss_pred -----hhHhhhHhhhhhhhhhhhhcccCCC
Q 029136 63 -----KDAAEHFMVQHASSLKRRRKCLKSG 87 (198)
Q Consensus 63 -----~d~v~Hit~qH~~~~Krrrr~rk~~ 87 (198)
..+..||+..|+..+|.+-+.+.+.
T Consensus 290 vf~~~~el~~h~~~~h~~~~~~~~~~~~~~ 319 (493)
T COG5236 290 VFPYHTELLEHLTRFHKVNARLSEIPRPGR 319 (493)
T ss_pred EeccHHHHHHHHHHHhhcccccCcCCCCcc
Confidence 2678888888888887666666554
No 8
>PHA00732 hypothetical protein
Probab=89.50 E-value=0.31 Score=36.25 Aligned_cols=42 Identities=26% Similarity=0.729 Sum_probs=31.5
Q ss_pred ecCCCCccch-hHHHHHhhhhhhccCCcccccccccccchhhhHhhhH
Q 029136 23 FPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHF 69 (198)
Q Consensus 23 F~CPfC~e~f-D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~d~v~Hi 69 (198)
|.|+.|++.| ....|..|....|.- ..|+.|...-. ++..|+
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 7899999855 678899998865542 26999988654 566665
No 9
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=89.26 E-value=0.26 Score=29.34 Aligned_cols=21 Identities=24% Similarity=0.608 Sum_probs=18.6
Q ss_pred eecCCCCccchhHHHHHhhhh
Q 029136 22 CFPCPFCYLEIEAHMICSHLQ 42 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~ 42 (198)
..+||+|+..|....|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 468999999999999999964
No 10
>PLN03086 PRLI-interacting factor K; Provisional
Probab=89.09 E-value=0.36 Score=47.62 Aligned_cols=47 Identities=21% Similarity=0.419 Sum_probs=36.3
Q ss_pred cceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccch-hhhHhhhHh
Q 029136 19 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL-GKDAAEHFM 70 (198)
Q Consensus 19 ~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v-~~d~v~Hit 70 (198)
+..-+.||+|++.|....|-.|....| +...|| |.... ..++..|++
T Consensus 450 l~~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~ 497 (567)
T PLN03086 450 AKNHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQA 497 (567)
T ss_pred cccCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhh
Confidence 334468999999888899999998866 678999 97543 357887874
No 11
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.09 E-value=0.3 Score=27.78 Aligned_cols=24 Identities=25% Similarity=0.627 Sum_probs=16.9
Q ss_pred ecCCCCccchhHHHHHhhhhhhcc
Q 029136 23 FPCPFCYLEIEAHMICSHLQEEHC 46 (198)
Q Consensus 23 F~CPfC~e~fD~~~Lc~H~~eeH~ 46 (198)
|.||+|...-....|-.|+...|+
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 789999653237789999988885
No 12
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=88.79 E-value=0.23 Score=48.22 Aligned_cols=35 Identities=29% Similarity=0.600 Sum_probs=30.5
Q ss_pred cCcceeecCCCCccchh-HHHHHhhhhhhccCCccc
Q 029136 17 DDVKACFPCPFCYLEIE-AHMICSHLQEEHCFEMKN 51 (198)
Q Consensus 17 dd~r~~F~CPfC~e~fD-~~~Lc~H~~eeH~~e~k~ 51 (198)
++++.-|.||+|.++|+ +..|-+|++.+|+.|...
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 67889999999988775 678999999999998764
No 13
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=87.36 E-value=0.36 Score=34.16 Aligned_cols=48 Identities=23% Similarity=0.582 Sum_probs=14.4
Q ss_pred cCCCCccc-hhHHHHHhhhhhhccCCcc---------------------cccccccccch--hhhHhhhHhh
Q 029136 24 PCPFCYLE-IEAHMICSHLQEEHCFEMK---------------------NAVCPLCAANL--GKDAAEHFMV 71 (198)
Q Consensus 24 ~CPfC~e~-fD~~~Lc~H~~eeH~~e~k---------------------~vVCPVCa~~v--~~d~v~Hit~ 71 (198)
.|+||... -+...|..|+...|.+... .-.|++|.... ...+..|++.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~ 72 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRS 72 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHH
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcC
Confidence 39999875 4578899999999987532 12399999975 4689999954
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=87.27 E-value=0.4 Score=26.69 Aligned_cols=21 Identities=19% Similarity=0.621 Sum_probs=13.1
Q ss_pred ecCCCCccch-hHHHHHhhhhh
Q 029136 23 FPCPFCYLEI-EAHMICSHLQE 43 (198)
Q Consensus 23 F~CPfC~e~f-D~~~Lc~H~~e 43 (198)
|.||.|++.| +...|..|+..
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 5677777633 45566666654
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=85.06 E-value=0.58 Score=33.36 Aligned_cols=27 Identities=26% Similarity=0.678 Sum_probs=16.8
Q ss_pred Ccccccccccccchh--hhHhhhHhhhhh
Q 029136 48 EMKNAVCPLCAANLG--KDAAEHFMVQHA 74 (198)
Q Consensus 48 e~k~vVCPVCa~~v~--~d~v~Hit~qH~ 74 (198)
...+..||+|.+.+. .|+-.|+.+.|.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~ 49 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHF 49 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhc
Confidence 345679999999754 799999976664
No 16
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=84.83 E-value=0.72 Score=37.17 Aligned_cols=40 Identities=23% Similarity=0.415 Sum_probs=26.4
Q ss_pred CcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 18 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 18 d~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
.-...|.||.|+..|+..+--...+ + ...-+||.|...+-
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEEE
Confidence 3467899999988666544332222 2 34489999998753
No 17
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=84.12 E-value=0.39 Score=30.11 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=22.6
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
.+|.||-|+..|++..-. .+....+||.|.+.
T Consensus 4 Y~y~C~~Cg~~fe~~~~~--------~~~~~~~CP~Cg~~ 35 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKI--------SDDPLATCPECGGD 35 (41)
T ss_pred EEEEcCCCCCEEEEEEec--------CCCCCCCCCCCCCc
Confidence 579999999877643211 12566889999984
No 18
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=83.03 E-value=0.61 Score=29.29 Aligned_cols=32 Identities=16% Similarity=0.286 Sum_probs=20.1
Q ss_pred ecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 23 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 23 F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
+.||.|+..|.+..- ..+.+...+.||.|...
T Consensus 3 ~~CP~C~~~~~v~~~------~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS------QLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHH------HcCCCCCEEECCCCCCE
Confidence 689999876555421 12233346889999765
No 19
>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=78.94 E-value=1.3 Score=29.48 Aligned_cols=32 Identities=22% Similarity=0.512 Sum_probs=22.5
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
.+|.|+-|+..|++. ....+ .....||.|...
T Consensus 4 Yey~C~~Cg~~fe~~---~~~~~-----~~~~~CP~Cg~~ 35 (52)
T TIGR02605 4 YEYRCTACGHRFEVL---QKMSD-----DPLATCPECGGE 35 (52)
T ss_pred EEEEeCCCCCEeEEE---EecCC-----CCCCCCCCCCCC
Confidence 579999999888853 11221 355789999973
No 20
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=78.22 E-value=0.93 Score=39.32 Aligned_cols=46 Identities=17% Similarity=0.612 Sum_probs=28.3
Q ss_pred ceeecCCCCccchh--HHHHHhh-----hhhhccC--------------CcccccccccccchhhhH
Q 029136 20 KACFPCPFCYLEIE--AHMICSH-----LQEEHCF--------------EMKNAVCPLCAANLGKDA 65 (198)
Q Consensus 20 r~~F~CPfC~e~fD--~~~Lc~H-----~~eeH~~--------------e~k~vVCPVCa~~v~~d~ 65 (198)
..+|.||.|.+.+. +.-.|-| |....-. ..+...||+|...++.+-
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 45799999966333 3344666 3333211 223468999999987533
No 21
>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=78.17 E-value=0.74 Score=38.62 Aligned_cols=56 Identities=18% Similarity=0.355 Sum_probs=29.0
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh-hhHhhhHhhhhhhhhh
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG-KDAAEHFMVQHASSLK 78 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~-~d~v~Hit~qH~~~~K 78 (198)
-.|.||.|+..+...++.. .+.-........||-|..... .-+...++++-|...+
T Consensus 17 l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~~~~~l~Nql~l~iR~~i~ 73 (188)
T PF08996_consen 17 LKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPLSPASLVNQLELQIREHIS 73 (188)
T ss_dssp EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B--HHHHHHHHHHHHHHHHH
T ss_pred eEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcCCHHHHHHHHHHHHHHHHH
Confidence 4899999998887777655 222223345578999999755 4555555555555443
No 22
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=77.81 E-value=2.3 Score=28.39 Aligned_cols=27 Identities=19% Similarity=0.115 Sum_probs=20.0
Q ss_pred ccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 29 YLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 29 ~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
+.-|+...+..++.. +..||+|.....
T Consensus 20 G~v~~~~~i~~~~~~-------~~~cP~~~~~~~ 46 (63)
T smart00504 20 GQTYERRAIEKWLLS-------HGTDPVTGQPLT 46 (63)
T ss_pred CCEEeHHHHHHHHHH-------CCCCCCCcCCCC
Confidence 445777878887765 468999988765
No 23
>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=77.78 E-value=1.6 Score=42.26 Aligned_cols=44 Identities=25% Similarity=0.287 Sum_probs=35.0
Q ss_pred ceeecCCCCcc-chhHHHHHhhhhhhccCCccc---ccccccccchhh
Q 029136 20 KACFPCPFCYL-EIEAHMICSHLQEEHCFEMKN---AVCPLCAANLGK 63 (198)
Q Consensus 20 r~~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~---vVCPVCa~~v~~ 63 (198)
+.--.||+|.+ -.|..++..|+..+|+..-.+ -+.|-+-...|.
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~~w~ 102 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDDDWA 102 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCHHHH
Confidence 45678999987 999999999999999997755 466766666553
No 24
>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=76.60 E-value=0.76 Score=29.97 Aligned_cols=34 Identities=26% Similarity=0.451 Sum_probs=20.3
Q ss_pred ecCCCCccchhHHHHHhhhhhhccCCcccccccccccchhhhHh
Q 029136 23 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAA 66 (198)
Q Consensus 23 F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~d~v 66 (198)
|.||.|+... + +. -.+....||+.|...+..+.+
T Consensus 1 m~Cp~Cg~~~-~------~~---D~~~g~~vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VF---DPERGELVCPNCGLVLEENII 34 (43)
T ss_dssp ESBTTTSSSE-E------EE---ETTTTEEEETTT-BBEE-TTB
T ss_pred CCCcCCcCCc-e------EE---cCCCCeEECCCCCCEeecccc
Confidence 6799997632 2 11 134556799999877765544
No 25
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=76.29 E-value=0.91 Score=33.34 Aligned_cols=32 Identities=28% Similarity=0.604 Sum_probs=20.6
Q ss_pred eecCCCCcc-chhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 22 CFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 22 ~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
.=|||||+. .+.+. |..-.-.++|.-|.+...
T Consensus 6 lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 6 VKPCPFCGCPSVTVK---------AISGYYRAKCNGCESRTG 38 (64)
T ss_pred ccCCCCCCCceeEEE---------ecCceEEEEcCCCCcCcc
Confidence 358999986 44433 222223489999999744
No 26
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=75.91 E-value=1.9 Score=30.38 Aligned_cols=26 Identities=23% Similarity=0.713 Sum_probs=21.1
Q ss_pred eeecCCCCccch-hHHHHHhhhhhhcc
Q 029136 21 ACFPCPFCYLEI-EAHMICSHLQEEHC 46 (198)
Q Consensus 21 ~~F~CPfC~e~f-D~~~Lc~H~~eeH~ 46 (198)
..|.|++|++.| +...|-.|+...+-
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCccC
Confidence 369999999877 79999999998643
No 27
>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=74.74 E-value=1.1 Score=28.29 Aligned_cols=24 Identities=33% Similarity=0.690 Sum_probs=12.7
Q ss_pred cCCCCccchhHHHHHhhhhhhccCCccccccccccc
Q 029136 24 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 59 (198)
Q Consensus 24 ~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~ 59 (198)
+||.|+.++.. .|....|||-|..
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 69999765544 5667789999974
No 28
>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=74.65 E-value=0.97 Score=31.84 Aligned_cols=30 Identities=33% Similarity=0.512 Sum_probs=21.4
Q ss_pred eecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
.|.||-|++.+++.... ..-.+.||.|.+.
T Consensus 2 ~~~CP~CG~~iev~~~~---------~GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPE---------LGELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCc---------cCCEEeCCCCCCE
Confidence 58999999977654322 1235789999886
No 29
>PHA00733 hypothetical protein
Probab=74.49 E-value=4.5 Score=32.30 Aligned_cols=48 Identities=21% Similarity=0.607 Sum_probs=32.3
Q ss_pred eecCCCCccchh-HHHHHhhhhhhccCCcccccccccccc--hhhhHhhhHhhhh
Q 029136 22 CFPCPFCYLEIE-AHMICSHLQEEHCFEMKNAVCPLCAAN--LGKDAAEHFMVQH 73 (198)
Q Consensus 22 ~F~CPfC~e~fD-~~~Lc~H~~eeH~~e~k~vVCPVCa~~--v~~d~v~Hit~qH 73 (198)
.|.|+.|+..|. ...|-.|..- | .....|++|... ...++..|+..-|
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 589999988655 4557778763 1 234689999775 3457888875444
No 30
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=74.18 E-value=0.78 Score=39.35 Aligned_cols=57 Identities=18% Similarity=0.326 Sum_probs=32.1
Q ss_pred eeecCCCCccchhHHHHHh--------------hhhhhccCCcccccccccccchhhhHhhhHhhhhhhhh
Q 029136 21 ACFPCPFCYLEIEAHMICS--------------HLQEEHCFEMKNAVCPLCAANLGKDAAEHFMVQHASSL 77 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~--------------H~~eeH~~e~k~vVCPVCa~~v~~d~v~Hit~qH~~~~ 77 (198)
-++.||+|+.+|....+.. |=.+.-|.==...|||-|.---..+...+++..-...+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~~~~~~~i 74 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLSPEQKEKI 74 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCCHHHHHHH
Confidence 3589999999887654332 22232232224478999987644332235544444434
No 31
>PLN03086 PRLI-interacting factor K; Provisional
Probab=72.39 E-value=3.5 Score=40.88 Aligned_cols=39 Identities=21% Similarity=0.548 Sum_probs=30.4
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
..+.|| |+..+....|-.|+. .||-+ +...|+.|...+.
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~-thCp~-Kpi~C~fC~~~v~ 515 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQA-STCPL-RLITCRFCGDMVQ 515 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhh-ccCCC-CceeCCCCCCccc
Confidence 458899 988888889999974 46653 7788999988763
No 32
>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=70.91 E-value=1.9 Score=26.87 Aligned_cols=25 Identities=32% Similarity=0.814 Sum_probs=16.1
Q ss_pred ecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 23 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 23 F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
|.|+-|+.-+|... .+-+||+|.+.
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCCc
Confidence 67888865444332 45689999763
No 33
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=70.25 E-value=1.9 Score=29.33 Aligned_cols=30 Identities=30% Similarity=0.721 Sum_probs=17.8
Q ss_pred ecCCCCcc-chhHHHHHhhhhhhccCCc---cccccccccc
Q 029136 23 FPCPFCYL-EIEAHMICSHLQEEHCFEM---KNAVCPLCAA 59 (198)
Q Consensus 23 F~CPfC~e-~fD~~~Lc~H~~eeH~~e~---k~vVCPVCa~ 59 (198)
-|||||+. .+-+.. ....+. -.+.|..|.+
T Consensus 4 kPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 58999975 433222 222222 3467999987
No 34
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=70.18 E-value=1.5 Score=30.69 Aligned_cols=13 Identities=38% Similarity=0.874 Sum_probs=10.0
Q ss_pred ecCCCCccchhHH
Q 029136 23 FPCPFCYLEIEAH 35 (198)
Q Consensus 23 F~CPfC~e~fD~~ 35 (198)
+.||||++.+++.
T Consensus 1 i~CPyCge~~~~~ 13 (52)
T PF14255_consen 1 IQCPYCGEPIEIL 13 (52)
T ss_pred CCCCCCCCeeEEE
Confidence 3699999977653
No 35
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=70.18 E-value=2.6 Score=27.71 Aligned_cols=29 Identities=24% Similarity=0.634 Sum_probs=18.4
Q ss_pred eecCCCCccchhHHHHHhhhhhhccCCcccccccccccch
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 61 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 61 (198)
+|.||-|+..++... . .....||-|..++
T Consensus 3 ~y~C~~CG~~~~~~~----------~-~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDE----------Y-GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECC----------C-CCceECCCCCCeE
Confidence 588888877665521 1 1157788887653
No 36
>PHA02768 hypothetical protein; Provisional
Probab=68.89 E-value=4.1 Score=28.94 Aligned_cols=34 Identities=21% Similarity=0.475 Sum_probs=21.9
Q ss_pred eecCCCCccch-hHHHHHhhhhhhccCCccccccccccc
Q 029136 22 CFPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAA 59 (198)
Q Consensus 22 ~F~CPfC~e~f-D~~~Lc~H~~eeH~~e~k~vVCPVCa~ 59 (198)
-|.||.|++.| ..+.|..|....+ ++--|..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~----k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN----TNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC----CcccCCcccc
Confidence 37888888744 5567888887744 3445555543
No 37
>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=66.72 E-value=3.7 Score=34.05 Aligned_cols=54 Identities=22% Similarity=0.405 Sum_probs=32.0
Q ss_pred eeecCCC----CccchhHHHHHhhhhhhccCCcccccccc----cccc-hhhhHhhhHhhhhhhhh
Q 029136 21 ACFPCPF----CYLEIEAHMICSHLQEEHCFEMKNAVCPL----CAAN-LGKDAAEHFMVQHASSL 77 (198)
Q Consensus 21 ~~F~CPf----C~e~fD~~~Lc~H~~eeH~~e~k~vVCPV----Ca~~-v~~d~v~Hit~qH~~~~ 77 (198)
-.|||+| |.+.+-......|.++ -. -++--||+ |.-. ...++..|++..|....
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~~-C~--~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEEE-CP--FRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHHT--T--TSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhcc-CC--CcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 4799999 9888888888888743 22 34577998 7543 34699999999998754
No 38
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=66.08 E-value=3 Score=26.42 Aligned_cols=26 Identities=31% Similarity=0.750 Sum_probs=17.2
Q ss_pred eecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
.|.|+-|+.-++-.. .+.+||||.+.
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 478999976443321 23599999874
No 39
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=65.35 E-value=4.1 Score=39.03 Aligned_cols=31 Identities=23% Similarity=0.762 Sum_probs=20.8
Q ss_pred CCCCccchhHH---------------HHHhhhhhhccCCcccccccccccc
Q 029136 25 CPFCYLEIEAH---------------MICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 25 CPfC~e~fD~~---------------~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
||.|-|++|+. .+..||.+. -||-||.|..+
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~~~irq~-----lngrcpacrr~ 62 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQN-----LNGRCPACRRK 62 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHHHHHHhh-----ccCCChHhhhh
Confidence 77777776654 233344433 68999999887
No 40
>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=64.53 E-value=5.2 Score=24.03 Aligned_cols=9 Identities=33% Similarity=1.136 Sum_probs=4.7
Q ss_pred cccccccch
Q 029136 53 VCPLCAANL 61 (198)
Q Consensus 53 VCPVCa~~v 61 (198)
.||||..++
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 355555554
No 41
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=63.46 E-value=4.5 Score=27.60 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=4.9
Q ss_pred ccccccchh
Q 029136 54 CPLCAANLG 62 (198)
Q Consensus 54 CPVCa~~v~ 62 (198)
||-|..+.+
T Consensus 1 CP~C~~kkk 9 (43)
T PF03470_consen 1 CPFCPGKKK 9 (43)
T ss_pred CCCCCCCCC
Confidence 555555544
No 42
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=62.93 E-value=2.8 Score=28.07 Aligned_cols=45 Identities=31% Similarity=0.612 Sum_probs=29.3
Q ss_pred eecCCC--CccchhHHHHHhhhhhhccCCcccccccc----cccchhh-hHhhh
Q 029136 22 CFPCPF--CYLEIEAHMICSHLQEEHCFEMKNAVCPL----CAANLGK-DAAEH 68 (198)
Q Consensus 22 ~F~CPf--C~e~fD~~~Lc~H~~eeH~~e~k~vVCPV----Ca~~v~~-d~v~H 68 (198)
...||+ |.+.+-...|-.|+..+=+. +.+.||. |..++.. ++..|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~--~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPK--RPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTT--SEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCC--CcEECCCCCCCCCCccchhHHhCC
Confidence 478999 77778888999999865444 4678999 9987654 55544
No 43
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=62.30 E-value=3.7 Score=30.08 Aligned_cols=27 Identities=26% Similarity=0.358 Sum_probs=20.8
Q ss_pred ccccccccc--hhhhHhhhHhhhhhhhhh
Q 029136 52 AVCPLCAAN--LGKDAAEHFMVQHASSLK 78 (198)
Q Consensus 52 vVCPVCa~~--v~~d~v~Hit~qH~~~~K 78 (198)
.-||-|.+. -.+|.+.|.+--|+++|-
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAHGWLFG 46 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHhhhhhc
Confidence 347777663 457999999999999984
No 44
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=60.41 E-value=3.7 Score=27.87 Aligned_cols=8 Identities=38% Similarity=0.999 Sum_probs=6.4
Q ss_pred cccccccc
Q 029136 53 VCPLCAAN 60 (198)
Q Consensus 53 VCPVCa~~ 60 (198)
.|+-|.+.
T Consensus 28 ~C~~Cga~ 35 (53)
T TIGR03655 28 ECSTCGAS 35 (53)
T ss_pred ECCCCCCC
Confidence 69988876
No 45
>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=60.07 E-value=3.4 Score=30.87 Aligned_cols=34 Identities=21% Similarity=0.602 Sum_probs=12.9
Q ss_pred ceeecCCCCc-c-chhHHHHHhhhhhhccCCcccccccccccc
Q 029136 20 KACFPCPFCY-L-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 20 r~~F~CPfC~-e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
-..|.||||+ + .+.+. ++ .....-.+.|-+|...
T Consensus 20 ~~~F~CPfC~~~~sV~v~-----id--kk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVK-----ID--KKEGIGILSCRVCGES 55 (81)
T ss_dssp SS----TTT--SS-EEEE-----EE--TTTTEEEEEESSS--E
T ss_pred CceEcCCcCCCCCeEEEE-----EE--ccCCEEEEEecCCCCe
Confidence 3689999997 4 22221 11 1122233669999765
No 46
>PRK12496 hypothetical protein; Provisional
Probab=59.50 E-value=5 Score=33.33 Aligned_cols=29 Identities=21% Similarity=0.438 Sum_probs=20.5
Q ss_pred ceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccch
Q 029136 20 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 61 (198)
Q Consensus 20 r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 61 (198)
+-.|.|+-|+..|+.. ....+||||...+
T Consensus 125 ~w~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~ 153 (164)
T PRK12496 125 KWRKVCKGCKKKYPED-------------YPDDVCEICGSPV 153 (164)
T ss_pred eeeEECCCCCccccCC-------------CCCCcCCCCCChh
Confidence 3468999999877532 2235899997654
No 47
>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=59.48 E-value=4.6 Score=26.39 Aligned_cols=31 Identities=26% Similarity=0.483 Sum_probs=22.4
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCccccccccccc
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 59 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~ 59 (198)
.+|.|+-|+..|++.. .+ .+...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~---~~-----~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQ---SI-----SEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEE---Ec-----CCCCCCcCCCCCC
Confidence 5799999998776541 11 2256789999987
No 48
>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=59.01 E-value=3.6 Score=24.22 Aligned_cols=10 Identities=30% Similarity=1.175 Sum_probs=8.5
Q ss_pred ecCCCCccch
Q 029136 23 FPCPFCYLEI 32 (198)
Q Consensus 23 F~CPfC~e~f 32 (198)
|.||+|+..|
T Consensus 15 ~~C~~C~k~F 24 (26)
T PF13465_consen 15 YKCPYCGKSF 24 (26)
T ss_dssp EEESSSSEEE
T ss_pred CCCCCCcCee
Confidence 9999998755
No 49
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=56.70 E-value=8.2 Score=35.43 Aligned_cols=37 Identities=19% Similarity=0.530 Sum_probs=25.8
Q ss_pred ceeecCCCCcc-chhHHHHHhhhhhhccCCcccccccccccc
Q 029136 20 KACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 20 r~~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
+..|.||+|++ .+-+..|--||...= -.-+|+||...
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~----l~c~C~iCGKa 196 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT----LPCECGICGKA 196 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC----CCccccccccc
Confidence 66788888876 788888888885432 23467777654
No 50
>PF12773 DZR: Double zinc ribbon
Probab=55.70 E-value=6.3 Score=25.79 Aligned_cols=27 Identities=26% Similarity=0.598 Sum_probs=17.8
Q ss_pred cCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 24 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 24 ~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
.||.|+..+. ..+....+||.|.+.+.
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 4666666555 34455678999888654
No 51
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=55.12 E-value=6.6 Score=28.48 Aligned_cols=32 Identities=28% Similarity=0.642 Sum_probs=22.5
Q ss_pred ceeecCCCCccc-hhHHHHHhhhhhhccCCcccccccccc
Q 029136 20 KACFPCPFCYLE-IEAHMICSHLQEEHCFEMKNAVCPLCA 58 (198)
Q Consensus 20 r~~F~CPfC~e~-fD~~~Lc~H~~eeH~~e~k~vVCPVCa 58 (198)
-..|.||-|++. +-. |..|.. ..+.-+||-|-
T Consensus 23 ~~~F~CPnCG~~~I~R---C~~CRk----~~~~Y~CP~CG 55 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR---CEKCRK----QSNPYTCPKCG 55 (59)
T ss_pred cCEeeCCCCCCeeEee---chhHHh----cCCceECCCCC
Confidence 578999999985 433 555533 35667899885
No 52
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=54.96 E-value=3.1 Score=32.29 Aligned_cols=15 Identities=33% Similarity=0.687 Sum_probs=11.6
Q ss_pred ccCcceeecCCCCcc
Q 029136 16 DDDVKACFPCPFCYL 30 (198)
Q Consensus 16 ddd~r~~F~CPfC~e 30 (198)
|....+.|.||||+.
T Consensus 30 e~~q~a~y~CpfCgk 44 (90)
T PTZ00255 30 EISQHAKYFCPFCGK 44 (90)
T ss_pred HHHHhCCccCCCCCC
Confidence 345678899999975
No 53
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=54.77 E-value=10 Score=34.75 Aligned_cols=52 Identities=19% Similarity=0.406 Sum_probs=38.7
Q ss_pred eecCCCCccchhHHHHH-hhhhhhccCCcccccccccccchh--hhHhhhHhhhhhhh
Q 029136 22 CFPCPFCYLEIEAHMIC-SHLQEEHCFEMKNAVCPLCAANLG--KDAAEHFMVQHASS 76 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc-~H~~eeH~~e~k~vVCPVCa~~v~--~d~v~Hit~qH~~~ 76 (198)
-+.|++|++-|+..=|. -|+ ..|-- -|+-.||.|..--. .|+-+||++ |+..
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHi-RTHTG-EKPF~C~hC~kAFADRSNLRAHmQT-HS~~ 241 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHI-RTHTG-EKPFSCPHCGKAFADRSNLRAHMQT-HSDV 241 (279)
T ss_pred CcccccccccccchHHhhccc-ccccC-CCCccCCcccchhcchHHHHHHHHh-hcCC
Confidence 48899999999977554 455 34544 47889999998755 599999964 5554
No 54
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=54.56 E-value=7.8 Score=40.32 Aligned_cols=43 Identities=21% Similarity=0.440 Sum_probs=36.7
Q ss_pred cceeecCCCCcc-chhHHHHHhhhhhhccCCcccccccccccch
Q 029136 19 VKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANL 61 (198)
Q Consensus 19 ~r~~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 61 (198)
.-+..+||||.. .-.+..|-.|+.-.|---.-|.-|+.|+..-
T Consensus 207 fsqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytF 250 (1007)
T KOG3623|consen 207 FSQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTF 250 (1007)
T ss_pred hhhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhh
Confidence 445689999988 5567899999999999888889999999863
No 55
>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=53.73 E-value=9 Score=25.84 Aligned_cols=24 Identities=25% Similarity=0.596 Sum_probs=19.7
Q ss_pred eecCCCCccchhHHHHHhhhhhhcc
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEHC 46 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH~ 46 (198)
.+.||.|...+.. .|..|+...|.
T Consensus 31 ~v~CPiC~~~~~~-~l~~Hl~~~H~ 54 (54)
T PF05605_consen 31 NVVCPICSSRVTD-NLIRHLNSQHR 54 (54)
T ss_pred CccCCCchhhhhh-HHHHHHHHhcC
Confidence 6999999876653 89999988874
No 56
>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=53.69 E-value=8.9 Score=25.93 Aligned_cols=22 Identities=23% Similarity=0.668 Sum_probs=10.7
Q ss_pred ccccccccchhh----hHhhhHhhhh
Q 029136 52 AVCPLCAANLGK----DAAEHFMVQH 73 (198)
Q Consensus 52 vVCPVCa~~v~~----d~v~Hit~qH 73 (198)
++||+|....+. +++.+++.+-
T Consensus 21 ~~CPlC~r~l~~e~~~~li~~~~~~i 46 (54)
T PF04423_consen 21 GCCPLCGRPLDEEHRQELIKKYKSEI 46 (54)
T ss_dssp EE-TTT--EE-HHHHHHHHHHHHHHH
T ss_pred CcCCCCCCCCCHHHHHHHHHHHHHHH
Confidence 388888877653 5565554433
No 57
>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=53.31 E-value=6.9 Score=30.86 Aligned_cols=35 Identities=20% Similarity=0.495 Sum_probs=25.7
Q ss_pred cCcceeecCCCCcc-chhHHHHHhhhhhhccCCcccccccccccchhhh
Q 029136 17 DDVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKD 64 (198)
Q Consensus 17 dd~r~~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~d 64 (198)
.+|.....||-|+. =||+. -.++|||-|.+-.-..
T Consensus 4 pelGtKR~Cp~CG~kFYDLn-------------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 4 PELGTKRTCPSCGAKFYDLN-------------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCcccCCCCcchhccCC-------------CCCccCCCCCCccCcc
Confidence 36777889999986 56643 3568999999865443
No 58
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=53.15 E-value=5.2 Score=30.14 Aligned_cols=26 Identities=35% Similarity=0.885 Sum_probs=16.5
Q ss_pred eecCCCCcc-chhHHHHHhhhhhhccCCcccccccccc
Q 029136 22 CFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCA 58 (198)
Q Consensus 22 ~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa 58 (198)
.|+||-|+. -|+.. .+...-+||||-
T Consensus 1 K~~CPCCg~~Tl~~~-----------~~~~ydIC~VC~ 27 (78)
T PF14206_consen 1 KYPCPCCGYYTLEER-----------GEGTYDICPVCF 27 (78)
T ss_pred CccCCCCCcEEeccC-----------CCcCceECCCCC
Confidence 379999954 44432 122356999996
No 59
>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=53.06 E-value=11 Score=31.03 Aligned_cols=35 Identities=26% Similarity=0.450 Sum_probs=23.6
Q ss_pred CcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 18 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 18 d~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
.-...|.||-|..-|.+.+-.. .+-.||+|....-
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEee
Confidence 3456799999986444433333 2678999999743
No 60
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.67 E-value=11 Score=31.67 Aligned_cols=34 Identities=24% Similarity=0.479 Sum_probs=22.7
Q ss_pred cceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 19 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 19 ~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
-...|.||-|+.-|...+-.. ..-.||+|....-
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCCe
Confidence 347899999976443333211 3578999999854
No 61
>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=52.60 E-value=10 Score=26.24 Aligned_cols=41 Identities=17% Similarity=0.335 Sum_probs=29.3
Q ss_pred CcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchhhhHhhhH
Q 029136 18 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHF 69 (198)
Q Consensus 18 d~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~d~v~Hi 69 (198)
+..+.=.||.|+.-... +...+..+||.|.....+|..+=+
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 44466789999752222 555667899999999888887755
No 62
>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=52.44 E-value=5.1 Score=27.85 Aligned_cols=45 Identities=22% Similarity=0.409 Sum_probs=27.4
Q ss_pred cccccccc-cCcceeecCCCCcc--chhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 9 IVDETEID-DDVKACFPCPFCYL--EIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 9 ~~de~e~d-dd~r~~F~CPfC~e--~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
.+||++.+ ++-..+|+|+ |+- .+....|-.+ .--+.|+-|+-.+.
T Consensus 4 ~l~d~~~~~~~~~~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 4 SLDDMEFDEEEGVYSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIR 51 (55)
T ss_dssp ETTTSEEETTTTEEEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEE
T ss_pred EhhhceecCCCCEEEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEE
Confidence 35666543 3335899996 975 5555555444 33467999997654
No 63
>PF15616 TerY-C: TerY-C metal binding domain
Probab=51.53 E-value=4.4 Score=33.23 Aligned_cols=46 Identities=17% Similarity=0.376 Sum_probs=32.0
Q ss_pred CcceeecCCCCccchhHHHHHhhhhhhccCCc-ccccccccccchhhhH
Q 029136 18 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEM-KNAVCPLCAANLGKDA 65 (198)
Q Consensus 18 d~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~-k~vVCPVCa~~v~~d~ 65 (198)
|+.-.=.||+|+..+-.+ ++=|-.-||.+. ..++||-|-.......
T Consensus 73 eL~g~PgCP~CGn~~~fa--~C~CGkl~Ci~g~~~~~CPwCg~~g~~~~ 119 (131)
T PF15616_consen 73 ELIGAPGCPHCGNQYAFA--VCGCGKLFCIDGEGEVTCPWCGNEGSFGA 119 (131)
T ss_pred HhcCCCCCCCCcChhcEE--EecCCCEEEeCCCCCEECCCCCCeeeecc
Confidence 344446899998765555 335888899644 5689999988755433
No 64
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=51.09 E-value=20 Score=25.55 Aligned_cols=28 Identities=18% Similarity=0.220 Sum_probs=18.7
Q ss_pred cchhHHHHHhhhhhhccCCcccccccccccchhh
Q 029136 30 LEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 63 (198)
Q Consensus 30 e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~ 63 (198)
.-||...+-.++.. ...+||+|...+..
T Consensus 24 ~tyer~~I~~~l~~------~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 24 HTYERSAIERWLEQ------NGGTDPFTRQPLSE 51 (73)
T ss_dssp EEEEHHHHHHHHCT------TSSB-TTT-SB-SG
T ss_pred CEEcHHHHHHHHHc------CCCCCCCCCCcCCc
Confidence 45777878777766 67899999777664
No 65
>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=50.89 E-value=8.1 Score=23.35 Aligned_cols=12 Identities=42% Similarity=0.977 Sum_probs=9.6
Q ss_pred cceeecCCCCcc
Q 029136 19 VKACFPCPFCYL 30 (198)
Q Consensus 19 ~r~~F~CPfC~e 30 (198)
.-..|+||-|++
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 356899999985
No 66
>PHA00616 hypothetical protein
Probab=49.28 E-value=12 Score=25.57 Aligned_cols=25 Identities=20% Similarity=0.223 Sum_probs=15.3
Q ss_pred ecCCCCcc-chhHHHHHhhhhhhccC
Q 029136 23 FPCPFCYL-EIEAHMICSHLQEEHCF 47 (198)
Q Consensus 23 F~CPfC~e-~fD~~~Lc~H~~eeH~~ 47 (198)
|.||-|+. =....+|-.|+...|--
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 56777766 34456666666666554
No 67
>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=48.95 E-value=4.3 Score=31.57 Aligned_cols=15 Identities=40% Similarity=0.798 Sum_probs=11.4
Q ss_pred ccCcceeecCCCCcc
Q 029136 16 DDDVKACFPCPFCYL 30 (198)
Q Consensus 16 ddd~r~~F~CPfC~e 30 (198)
|....+.|.||||+.
T Consensus 29 e~~q~a~y~CpfCgk 43 (91)
T TIGR00280 29 EIQQKAKYVCPFCGK 43 (91)
T ss_pred HHHHhcCccCCCCCC
Confidence 345678899999965
No 68
>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=48.50 E-value=13 Score=21.21 Aligned_cols=23 Identities=17% Similarity=0.339 Sum_probs=15.2
Q ss_pred ecCCCCccch-hHHHHHhhhhhhc
Q 029136 23 FPCPFCYLEI-EAHMICSHLQEEH 45 (198)
Q Consensus 23 F~CPfC~e~f-D~~~Lc~H~~eeH 45 (198)
|.|..|++.| +...|..|....|
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 6788887744 5667777775444
No 69
>PF13395 HNH_4: HNH endonuclease
Probab=48.06 E-value=8.8 Score=26.08 Aligned_cols=14 Identities=29% Similarity=0.778 Sum_probs=11.6
Q ss_pred CCCCccchhHHHHH
Q 029136 25 CPFCYLEIEAHMIC 38 (198)
Q Consensus 25 CPfC~e~fD~~~Lc 38 (198)
||||++.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 89999988888763
No 70
>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=48.02 E-value=11 Score=23.97 Aligned_cols=25 Identities=24% Similarity=0.450 Sum_probs=10.3
Q ss_pred eeecCCCCccchhH-----HHHHhhhhhhc
Q 029136 21 ACFPCPFCYLEIEA-----HMICSHLQEEH 45 (198)
Q Consensus 21 ~~F~CPfC~e~fD~-----~~Lc~H~~eeH 45 (198)
....|-||...+.. ..|-.|+...|
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 34455566544333 24555554444
No 71
>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=47.00 E-value=11 Score=24.19 Aligned_cols=17 Identities=29% Similarity=0.675 Sum_probs=7.5
Q ss_pred cccccccchh-hhHhhhH
Q 029136 53 VCPLCAANLG-KDAAEHF 69 (198)
Q Consensus 53 VCPVCa~~v~-~d~v~Hi 69 (198)
.||.|...+. .-|..|+
T Consensus 6 ~C~nC~R~v~a~RfA~HL 23 (33)
T PF08209_consen 6 ECPNCGRPVAASRFAPHL 23 (33)
T ss_dssp E-TTTSSEEEGGGHHHHH
T ss_pred ECCCCcCCcchhhhHHHH
Confidence 4555555443 2444444
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=46.85 E-value=7.5 Score=30.41 Aligned_cols=31 Identities=23% Similarity=0.415 Sum_probs=22.7
Q ss_pred cCcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 17 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 17 dd~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
++....+.|+-|+..+..... ...||.|...
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 65 EDEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred EeeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 345678999999887766532 4679999874
No 73
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=46.35 E-value=4.9 Score=31.18 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=10.9
Q ss_pred cCcceeecCCCCcc
Q 029136 17 DDVKACFPCPFCYL 30 (198)
Q Consensus 17 dd~r~~F~CPfC~e 30 (198)
....+.|.||||+.
T Consensus 31 ~~q~a~y~CpfCgk 44 (90)
T PRK03976 31 EKMRAKHVCPVCGR 44 (90)
T ss_pred HHHhcCccCCCCCC
Confidence 44568899999965
No 74
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=45.98 E-value=11 Score=25.26 Aligned_cols=28 Identities=21% Similarity=0.392 Sum_probs=20.4
Q ss_pred eecCCCCccchhHHHHHhhhhhhccCCcccccccccccch
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 61 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 61 (198)
.|.|.-|+.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58899998877754 33457899997654
No 75
>smart00355 ZnF_C2H2 zinc finger.
Probab=45.51 E-value=18 Score=19.13 Aligned_cols=20 Identities=20% Similarity=0.556 Sum_probs=10.5
Q ss_pred ecCCCCccch-hHHHHHhhhh
Q 029136 23 FPCPFCYLEI-EAHMICSHLQ 42 (198)
Q Consensus 23 F~CPfC~e~f-D~~~Lc~H~~ 42 (198)
|.|+.|+..| ....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 4566665533 3345555554
No 76
>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=43.81 E-value=8.3 Score=29.97 Aligned_cols=31 Identities=29% Similarity=0.505 Sum_probs=19.7
Q ss_pred cCcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 17 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 17 dd~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
+.....+.|+-|+.+|+...... .||-|...
T Consensus 65 e~~p~~~~C~~Cg~~~~~~~~~~-------------~CP~Cgs~ 95 (113)
T PF01155_consen 65 EEVPARARCRDCGHEFEPDEFDF-------------SCPRCGSP 95 (113)
T ss_dssp EEE--EEEETTTS-EEECHHCCH-------------H-SSSSSS
T ss_pred EecCCcEECCCCCCEEecCCCCC-------------CCcCCcCC
Confidence 34567899999998887765432 29999875
No 77
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=43.52 E-value=11 Score=30.13 Aligned_cols=37 Identities=24% Similarity=0.493 Sum_probs=19.9
Q ss_pred cceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 19 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 19 ~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
+..+|.||||+-+-=.+-+ -.--.---.++|-+|-..
T Consensus 19 L~k~FtCp~Cghe~vs~ct-----vkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCT-----VKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred CCceEecCccCCeeeeEEE-----EEecCceeEEEcccCcce
Confidence 3458999999653222111 011111234679998765
No 78
>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=43.06 E-value=6.2 Score=32.63 Aligned_cols=13 Identities=23% Similarity=0.513 Sum_probs=10.9
Q ss_pred CcceeecCCCCcc
Q 029136 18 DVKACFPCPFCYL 30 (198)
Q Consensus 18 d~r~~F~CPfC~e 30 (198)
|+...|.|||||-
T Consensus 4 d~~~D~vcPwcyl 16 (209)
T cd03021 4 ELYYDVVSPYSYL 16 (209)
T ss_pred EEEEeCCChHHHH
Confidence 4678899999976
No 79
>smart00507 HNHc HNH nucleases.
Probab=42.24 E-value=4.3 Score=25.07 Aligned_cols=21 Identities=14% Similarity=0.316 Sum_probs=13.4
Q ss_pred ecCCCCccchhHHHHHhhhhh
Q 029136 23 FPCPFCYLEIEAHMICSHLQE 43 (198)
Q Consensus 23 F~CPfC~e~fD~~~Lc~H~~e 43 (198)
+.|+||++.++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 789999886653223455554
No 80
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=42.21 E-value=11 Score=29.75 Aligned_cols=9 Identities=44% Similarity=1.331 Sum_probs=7.4
Q ss_pred eecCCCCcc
Q 029136 22 CFPCPFCYL 30 (198)
Q Consensus 22 ~F~CPfC~e 30 (198)
.++||||++
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 468999987
No 81
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.98 E-value=17 Score=36.94 Aligned_cols=30 Identities=23% Similarity=0.438 Sum_probs=25.9
Q ss_pred cceeecCCCCcc-chhHHHHHhhhhhhccCC
Q 029136 19 VKACFPCPFCYL-EIEAHMICSHLQEEHCFE 48 (198)
Q Consensus 19 ~r~~F~CPfC~e-~fD~~~Lc~H~~eeH~~e 48 (198)
.+.--.|+||-+ -||..+|..|+..+|.++
T Consensus 179 ~rGhp~C~~C~~~fld~~el~rH~~~~h~~c 209 (669)
T KOG2231|consen 179 CRGHPLCKFCHERFLDDDELYRHLRFDHEFC 209 (669)
T ss_pred ccCCccchhhhhhhccHHHHHHhhccceehe
Confidence 455678999976 999999999999999885
No 82
>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=41.72 E-value=17 Score=25.39 Aligned_cols=8 Identities=38% Similarity=1.393 Sum_probs=3.8
Q ss_pred eecCCCCc
Q 029136 22 CFPCPFCY 29 (198)
Q Consensus 22 ~F~CPfC~ 29 (198)
.|.||+|+
T Consensus 44 ~y~C~~Cg 51 (54)
T PF10058_consen 44 QYRCPYCG 51 (54)
T ss_pred EEEcCCCC
Confidence 44455543
No 83
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=41.21 E-value=25 Score=25.78 Aligned_cols=34 Identities=32% Similarity=0.603 Sum_probs=20.5
Q ss_pred CcceeecCCCCcc-chhHHHHHhhhhhhccCCcccccccccc
Q 029136 18 DVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCA 58 (198)
Q Consensus 18 d~r~~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa 58 (198)
|--..|+||-|+| .+-.-.-|. --.+.-+||-|-
T Consensus 23 e~~v~F~CPnCGe~~I~Rc~~CR-------k~g~~Y~Cp~CG 57 (61)
T COG2888 23 ETAVKFPCPNCGEVEIYRCAKCR-------KLGNPYRCPKCG 57 (61)
T ss_pred CceeEeeCCCCCceeeehhhhHH-------HcCCceECCCcC
Confidence 4456899999996 443322222 124556788884
No 84
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=41.16 E-value=11 Score=30.41 Aligned_cols=25 Identities=32% Similarity=0.797 Sum_probs=15.6
Q ss_pred cCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 24 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 24 ~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
+||-|..+|-- -+....|||-|+--
T Consensus 4 ~CP~C~seytY------------~dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTY------------HDGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceE------------ecCCeeECcccccc
Confidence 68888544321 14456789999864
No 85
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.64 E-value=20 Score=30.10 Aligned_cols=35 Identities=20% Similarity=0.455 Sum_probs=27.5
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchhhhHhhhHhh
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHFMV 71 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~d~v~Hit~ 71 (198)
+.=.||-|+. ...+...||.|....-+|..+=++.
T Consensus 308 tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~Ni 342 (364)
T COG0675 308 TSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALNI 342 (364)
T ss_pred CcccccccCC----------------ccceeEECCCCCCeehhhHHHHHHH
Confidence 3367999987 3356789999999988888887744
No 86
>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=40.22 E-value=8.5 Score=30.72 Aligned_cols=24 Identities=25% Similarity=0.632 Sum_probs=16.3
Q ss_pred CcceeecCCCCcc-chhHHHHHhhh
Q 029136 18 DVKACFPCPFCYL-EIEAHMICSHL 41 (198)
Q Consensus 18 d~r~~F~CPfC~e-~fD~~~Lc~H~ 41 (198)
|+-.+|.||||+. .-.+..+....
T Consensus 2 ~~~~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 2 DIWSDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred eEEecCcCccHHHHHHHHHHHHHhC
Confidence 3567899999986 44555565554
No 87
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=39.47 E-value=20 Score=25.68 Aligned_cols=47 Identities=17% Similarity=0.293 Sum_probs=22.3
Q ss_pred cCcceeecCC--CCccchhHHHHHhhhhhhcc----CCcccccccccccchhh
Q 029136 17 DDVKACFPCP--FCYLEIEAHMICSHLQEEHC----FEMKNAVCPLCAANLGK 63 (198)
Q Consensus 17 dd~r~~F~CP--fC~e~fD~~~Lc~H~~eeH~----~e~k~vVCPVCa~~v~~ 63 (198)
++-.+...|| -|+.-|=..-|...+..... +.+..|.||.|...+.-
T Consensus 15 ~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 15 DGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp T-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 3344678887 88888888888888876544 34556779999987653
No 88
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=39.43 E-value=17 Score=21.48 Aligned_cols=10 Identities=50% Similarity=0.923 Sum_probs=6.2
Q ss_pred ecCCCCccch
Q 029136 23 FPCPFCYLEI 32 (198)
Q Consensus 23 F~CPfC~e~f 32 (198)
-.||.|+..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 3577776543
No 89
>PRK12495 hypothetical protein; Provisional
Probab=39.35 E-value=15 Score=32.93 Aligned_cols=30 Identities=20% Similarity=0.331 Sum_probs=21.8
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchhh
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 63 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~ 63 (198)
..|.||.|+..+- .. ...++||+|-..+..
T Consensus 41 sa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIF------------RH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCccc------------CC-CCeeECCCCCCcccc
Confidence 3589999988654 22 445779999988763
No 90
>PRK03922 hypothetical protein; Provisional
Probab=39.27 E-value=13 Score=30.15 Aligned_cols=14 Identities=21% Similarity=0.422 Sum_probs=11.3
Q ss_pred eecCCCCccchhHH
Q 029136 22 CFPCPFCYLEIEAH 35 (198)
Q Consensus 22 ~F~CPfC~e~fD~~ 35 (198)
.-.||+|+++||-.
T Consensus 49 ~~~cP~cge~~~~a 62 (113)
T PRK03922 49 LTICPKCGEPFDSA 62 (113)
T ss_pred cccCCCCCCcCCcE
Confidence 35799999998854
No 91
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.95 E-value=14 Score=29.21 Aligned_cols=41 Identities=22% Similarity=0.674 Sum_probs=24.0
Q ss_pred cceeecCCCCccchhHH-HH-HhhhhhhccCCc---cccccccccc
Q 029136 19 VKACFPCPFCYLEIEAH-MI-CSHLQEEHCFEM---KNAVCPLCAA 59 (198)
Q Consensus 19 ~r~~F~CPfC~e~fD~~-~L-c~H~~eeH~~e~---k~vVCPVCa~ 59 (198)
+...+.||.|.+.|... .| |-|---..|... ....||.|..
T Consensus 10 ~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred ccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 44569999998766655 22 233222222222 3488999993
No 92
>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=38.92 E-value=7.7 Score=30.11 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=9.9
Q ss_pred cCcceeecCCCCcc
Q 029136 17 DDVKACFPCPFCYL 30 (198)
Q Consensus 17 dd~r~~F~CPfC~e 30 (198)
....+.|.||||+.
T Consensus 30 ~~q~~ky~Cp~Cgk 43 (90)
T PF01780_consen 30 ISQHAKYTCPFCGK 43 (90)
T ss_dssp HHHHS-BEESSSSS
T ss_pred HHHhCCCcCCCCCC
Confidence 34567899999976
No 93
>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=38.55 E-value=8.3 Score=30.38 Aligned_cols=37 Identities=16% Similarity=0.033 Sum_probs=21.2
Q ss_pred CCchhhHHhhhHHHHHHHhcccccccchhhhhhhheeee
Q 029136 157 PPSSEYKLLWSQLLFKKLANKISVSSTMHFKIDVLLVIG 195 (198)
Q Consensus 157 ~~~~~~k~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (198)
..+..++....+.. +.+.+.-|.++-.|+++==.++|
T Consensus 144 ~~~~~~~~~l~~~~--~~a~~~gi~gvPtfvv~g~~~~G 180 (192)
T cd03022 144 ADDPAVKAALRANT--EEAIARGVFGVPTFVVDGEMFWG 180 (192)
T ss_pred cCCHHHHHHHHHHH--HHHHHcCCCcCCeEEECCeeecc
Confidence 34445565555544 33456677888888776434443
No 94
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=38.36 E-value=27 Score=33.98 Aligned_cols=59 Identities=24% Similarity=0.371 Sum_probs=34.5
Q ss_pred ccccccCcceeecCCCCcc---chhHHHHHhhhhhhccCCccccccccccc--------chh---hhHhhhHhhhhhhhh
Q 029136 12 ETEIDDDVKACFPCPFCYL---EIEAHMICSHLQEEHCFEMKNAVCPLCAA--------NLG---KDAAEHFMVQHASSL 77 (198)
Q Consensus 12 e~e~ddd~r~~F~CPfC~e---~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~--------~v~---~d~v~Hit~qH~~~~ 77 (198)
+.+.++.-++.|.||+|.. .+|...|..- +.-.-.|-.|-. ++. ...+++++-|--.++
T Consensus 118 d~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~-------~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~~~~Q~~pi~ 190 (436)
T KOG2593|consen 118 DRLRDDTNVAGYVCPNCQKKYTSLEALQLLDN-------ETGEFHCENCGGELVEDENKLPSKESRTALNRLMEQLEPII 190 (436)
T ss_pred HHhhhccccccccCCccccchhhhHHHHhhcc-------cCceEEEecCCCchhcccccCchHHHHHHHHHHHHHHHHHH
Confidence 3334455678999999965 5666666542 222335666544 333 355677766655554
No 95
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=38.36 E-value=14 Score=30.74 Aligned_cols=32 Identities=28% Similarity=0.597 Sum_probs=19.0
Q ss_pred cCCCCccchhHHHHHhhhhhhccCCccccc-----ccccccch
Q 029136 24 PCPFCYLEIEAHMICSHLQEEHCFEMKNAV-----CPLCAANL 61 (198)
Q Consensus 24 ~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vV-----CPVCa~~v 61 (198)
.||||+... .|..+.-.....|+| ||-|.-.-
T Consensus 2 ~cp~c~~~~------~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPD------TRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCC------CEeEeccccCCCCceeeeeeccccCCcc
Confidence 699997533 133344444444444 99998763
No 96
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=38.21 E-value=14 Score=29.52 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=11.3
Q ss_pred eecCCCCccchhHH
Q 029136 22 CFPCPFCYLEIEAH 35 (198)
Q Consensus 22 ~F~CPfC~e~fD~~ 35 (198)
.-.||+|++++|-.
T Consensus 47 ~~~cP~Cge~~~~a 60 (102)
T PF04475_consen 47 DTICPKCGEELDSA 60 (102)
T ss_pred cccCCCCCCccCce
Confidence 36899999998854
No 97
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.92 E-value=24 Score=30.80 Aligned_cols=41 Identities=20% Similarity=0.660 Sum_probs=25.5
Q ss_pred eeecCCCCccchhHHH---------HHhhhhhhccCCcccccccccccchhh
Q 029136 21 ACFPCPFCYLEIEAHM---------ICSHLQEEHCFEMKNAVCPLCAANLGK 63 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~---------Lc~H~~eeH~~e~k~vVCPVCa~~v~~ 63 (198)
+.|.||-|-..+..-. .|.-|..+=- .+..+||+|..++..
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~al--k~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDAL--KNTNKCPTCRKKITH 179 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHH--HhCCCCCCcccccch
Confidence 5799999965444332 3444433321 234789999998764
No 98
>PHA02929 N1R/p28-like protein; Provisional
Probab=37.83 E-value=6.4 Score=34.97 Aligned_cols=43 Identities=19% Similarity=0.520 Sum_probs=24.5
Q ss_pred ceeecCCCCccchhHH----------HHHhhhhhhccC---Ccccccccccccchh
Q 029136 20 KACFPCPFCYLEIEAH----------MICSHLQEEHCF---EMKNAVCPLCAANLG 62 (198)
Q Consensus 20 r~~F~CPfC~e~fD~~----------~Lc~H~~eeH~~---e~k~vVCPVCa~~v~ 62 (198)
..+..||.|.+++... .=|.|.--..|. -.....||+|...+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 4467999998765321 125553222222 124568999987643
No 99
>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=37.22 E-value=18 Score=35.22 Aligned_cols=49 Identities=18% Similarity=0.314 Sum_probs=36.6
Q ss_pred chhHHHHHhhhhhhccCCcc-----------------cccccccccch--hhhHhhhHhhhhhhhhhh
Q 029136 31 EIEAHMICSHLQEEHCFEMK-----------------NAVCPLCAANL--GKDAAEHFMVQHASSLKR 79 (198)
Q Consensus 31 ~fD~~~Lc~H~~eeH~~e~k-----------------~vVCPVCa~~v--~~d~v~Hit~qH~~~~Kr 79 (198)
.+.+..|-.|+...|-.++. .-+||+|+.+- ..++..|+-.+|..-++.
T Consensus 20 kVsi~eL~sy~~~~~~~~a~~~Lseal~fak~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P 87 (466)
T PF04780_consen 20 KVSIDELKSYYESVYDREAADALSEALSFAKENKSWRFWICPRCSKKFSDAESCLSHMEQEHPAGLKP 87 (466)
T ss_pred eeEHHHHHHHHHhccchHHHHHHHHHHHHHHhcCceeEeeCCcccceeCCHHHHHHHHHHhhhhhcCh
Confidence 46677888888877654332 23599999763 369999999999998863
No 100
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=36.83 E-value=14 Score=28.96 Aligned_cols=31 Identities=29% Similarity=0.396 Sum_probs=21.3
Q ss_pred cCcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 17 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 17 dd~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
+++...+.|+-|+..|.... ....||-|...
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred EeeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 44567899999987665432 33469999864
No 101
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=36.60 E-value=26 Score=23.27 Aligned_cols=26 Identities=19% Similarity=0.433 Sum_probs=16.3
Q ss_pred eeecCCCCccchhHH------HHHhhhhhhcc
Q 029136 21 ACFPCPFCYLEIEAH------MICSHLQEEHC 46 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~------~Lc~H~~eeH~ 46 (198)
+.-.|-+|...+... .|..|+...||
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 566778886655443 56666666555
No 102
>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=36.57 E-value=18 Score=34.72 Aligned_cols=35 Identities=31% Similarity=0.813 Sum_probs=17.7
Q ss_pred ceeecCCCCccchhHHHHHhhhhhhccCCccccccccccc-chhhhHhh
Q 029136 20 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA-NLGKDAAE 67 (198)
Q Consensus 20 r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~-~v~~d~v~ 67 (198)
.+.-.||||+-.|. | +-+.-+||||-- .||.+.+|
T Consensus 378 ~~~v~CP~cgA~y~------------~-~~kG~lC~vC~l~~IG~~a~G 413 (422)
T PF06957_consen 378 SPSVKCPYCGAKYH------------P-EYKGQLCPVCELSEIGADASG 413 (422)
T ss_dssp S-EEE-TTT--EEE------------G-GGTTSB-TTTTTBBTT---S-
T ss_pred CCCeeCCCCCCccC------------h-hhCCCCCCCCcceeeCCccee
Confidence 34567999976442 2 356789999986 57776654
No 103
>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=36.46 E-value=21 Score=28.95 Aligned_cols=37 Identities=27% Similarity=0.481 Sum_probs=27.1
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
.+..|.-|+..++...+......+.. ..||.|...+-
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~~-----~~C~~C~~~lr 140 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEEP-----PRCPKCGGLLR 140 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTSS-----CBCTTTSCBEE
T ss_pred ceeeecCCCccccchhhccccccccc-----ccccccCccCC
Confidence 35799999998888777665554433 29999999644
No 104
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=36.38 E-value=19 Score=28.78 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=19.3
Q ss_pred cccccccccchh-----hhHhhhHhhhhhhh
Q 029136 51 NAVCPLCAANLG-----KDAAEHFMVQHASS 76 (198)
Q Consensus 51 ~vVCPVCa~~v~-----~d~v~Hit~qH~~~ 76 (198)
.|.||+|....| ..+..|++.-||=.
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~ 55 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGIS 55 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhccccc
Confidence 789999997655 35788887777643
No 105
>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=36.02 E-value=21 Score=21.62 Aligned_cols=8 Identities=50% Similarity=1.173 Sum_probs=4.3
Q ss_pred CCCCccch
Q 029136 25 CPFCYLEI 32 (198)
Q Consensus 25 CPfC~e~f 32 (198)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 55555544
No 106
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=35.32 E-value=11 Score=26.93 Aligned_cols=10 Identities=40% Similarity=0.916 Sum_probs=6.8
Q ss_pred ceeecCCCCc
Q 029136 20 KACFPCPFCY 29 (198)
Q Consensus 20 r~~F~CPfC~ 29 (198)
+..|.||.||
T Consensus 12 ~v~~~Cp~cG 21 (55)
T PF13824_consen 12 HVNFECPDCG 21 (55)
T ss_pred ccCCcCCCCC
Confidence 4567777774
No 107
>PRK11595 DNA utilization protein GntX; Provisional
Probab=35.25 E-value=19 Score=30.76 Aligned_cols=35 Identities=23% Similarity=0.477 Sum_probs=21.0
Q ss_pred cCCCCccchhH--HHHHhhhhhhccCCcccccccccccc
Q 029136 24 PCPFCYLEIEA--HMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 24 ~CPfC~e~fD~--~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
.|+.|++.+.. ..||.+|.+.=+.- ...||.|...
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 48888765532 35888887653331 2467777643
No 108
>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=34.55 E-value=18 Score=24.72 Aligned_cols=12 Identities=33% Similarity=0.858 Sum_probs=5.2
Q ss_pred CcceeecCCCCc
Q 029136 18 DVKACFPCPFCY 29 (198)
Q Consensus 18 d~r~~F~CPfC~ 29 (198)
++-.+|.||-|+
T Consensus 30 ~Lp~~w~CP~C~ 41 (47)
T PF00301_consen 30 DLPDDWVCPVCG 41 (47)
T ss_dssp GS-TT-B-TTTS
T ss_pred HCCCCCcCcCCC
Confidence 445556666664
No 109
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.37 E-value=19 Score=28.92 Aligned_cols=18 Identities=22% Similarity=0.357 Sum_probs=13.3
Q ss_pred CcceeecCCCCccchhHH
Q 029136 18 DVKACFPCPFCYLEIEAH 35 (198)
Q Consensus 18 d~r~~F~CPfC~e~fD~~ 35 (198)
.....+.|+-|+..+...
T Consensus 66 ~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred ecceEEECCCCCCEEecc
Confidence 456789999998765543
No 110
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=34.22 E-value=21 Score=33.56 Aligned_cols=40 Identities=20% Similarity=0.401 Sum_probs=30.5
Q ss_pred eeecCCCCccchh--HHHHHhhhhhh-ccCC-----cccccccccccc
Q 029136 21 ACFPCPFCYLEIE--AHMICSHLQEE-HCFE-----MKNAVCPLCAAN 60 (198)
Q Consensus 21 ~~F~CPfC~e~fD--~~~Lc~H~~ee-H~~e-----~k~vVCPVCa~~ 60 (198)
.+-.||.|+.+.| +.+||.=|.-+ |+.. .+-.+|+.|-+.
T Consensus 5 ~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~ 52 (355)
T COG1499 5 STILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGAY 52 (355)
T ss_pred cccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCCc
Confidence 4568999999888 88999888766 5553 344789999864
No 111
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=33.99 E-value=12 Score=21.94 Aligned_cols=6 Identities=50% Similarity=1.237 Sum_probs=3.4
Q ss_pred CCCCcc
Q 029136 25 CPFCYL 30 (198)
Q Consensus 25 CPfC~e 30 (198)
||.|+.
T Consensus 2 Cp~CG~ 7 (23)
T PF13240_consen 2 CPNCGA 7 (23)
T ss_pred CcccCC
Confidence 566654
No 112
>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=32.92 E-value=23 Score=29.32 Aligned_cols=32 Identities=19% Similarity=0.206 Sum_probs=23.8
Q ss_pred CcceeecCCCCcc-chhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 18 DVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 18 d~r~~F~CPfC~e-~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
++.....||-|+. =||+. ..++|||-|..-.-
T Consensus 5 elGtKr~Cp~cg~kFYDLn-------------k~p~vcP~cg~~~~ 37 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDLN-------------RRPAVSPYTGEQFP 37 (129)
T ss_pred hhCccccCCCcCccccccC-------------CCCccCCCcCCccC
Confidence 5677889999986 55542 35799999987643
No 113
>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=31.85 E-value=25 Score=32.69 Aligned_cols=39 Identities=23% Similarity=0.487 Sum_probs=24.5
Q ss_pred ecCCCCcc----chhH--------HHHHhhhhhhccCCcccccccccccchh
Q 029136 23 FPCPFCYL----EIEA--------HMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 23 F~CPfC~e----~fD~--------~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
+.||.|.. +=+. ..+|..|.+..- ....+.||+|...+.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~-~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLF-VRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHh-cCCCCCCCCCCCccc
Confidence 68999944 3332 135666776663 334578999977543
No 114
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=31.41 E-value=12 Score=32.26 Aligned_cols=32 Identities=19% Similarity=0.438 Sum_probs=20.3
Q ss_pred eecCCCCccchhHHHHHhhhhhhccCC-ccccc
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEHCFE-MKNAV 53 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH~~e-~k~vV 53 (198)
.|.||.|...+.+..=--+|...|.|| +|.|.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCCccccCce
Confidence 389999988664322223467788885 44554
No 115
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=31.17 E-value=16 Score=32.48 Aligned_cols=43 Identities=19% Similarity=0.089 Sum_probs=28.6
Q ss_pred cccCCCCchhhHHhhhHHHHHHHhcccccccchhhhh-hhheeeec
Q 029136 152 DLKRYPPSSEYKLLWSQLLFKKLANKISVSSTMHFKI-DVLLVIGI 196 (198)
Q Consensus 152 ~~~r~~~~~~~k~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~ 196 (198)
..++-..+..|+...-+-. +.+.++-|+..-.|++ |=+.|-|.
T Consensus 156 ~~~~~L~s~~~~~avr~d~--~~A~e~gI~gVP~fv~d~~~~V~Ga 199 (225)
T COG2761 156 EFKADLASDAAKDAVRQDE--AAAQEMGIRGVPTFVFDGKYAVSGA 199 (225)
T ss_pred HHHHHHhChHHHHHHHHHH--HHHHHCCCccCceEEEcCcEeecCC
Confidence 3566667777777655543 2567788888888888 55555554
No 116
>PRK00420 hypothetical protein; Validated
Probab=30.81 E-value=30 Score=27.65 Aligned_cols=28 Identities=25% Similarity=0.510 Sum_probs=18.2
Q ss_pred eecCCCCccchhHHHHHhhhhhhccCCcccccccccccch
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 61 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 61 (198)
.-.||.|+-.+= .+.....+||+|..-+
T Consensus 23 ~~~CP~Cg~pLf------------~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 23 SKHCPVCGLPLF------------ELKDGEVVCPVHGKVY 50 (112)
T ss_pred cCCCCCCCCcce------------ecCCCceECCCCCCee
Confidence 368999974321 1124468999999864
No 117
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.34 E-value=22 Score=38.03 Aligned_cols=38 Identities=24% Similarity=0.504 Sum_probs=24.2
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
..|.||.|+..-...--|..| ........||-|-..+.
T Consensus 637 ~~frCP~CG~~Te~i~fCP~C----G~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRC----GIEVEEDECEKCGREPT 674 (1121)
T ss_pred CcccCCCCCCCCCcceeCccc----cCcCCCCcCCCCCCCCC
Confidence 457777777654555566666 33344466888888754
No 118
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=30.31 E-value=17 Score=33.81 Aligned_cols=19 Identities=16% Similarity=0.427 Sum_probs=15.3
Q ss_pred ccccccccccchhhhHhhh
Q 029136 50 KNAVCPLCAANLGKDAAEH 68 (198)
Q Consensus 50 k~vVCPVCa~~v~~d~v~H 68 (198)
+..+||||..+|...||.-
T Consensus 184 ~~~~CPvCGS~PvaSmV~~ 202 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQI 202 (308)
T ss_pred ccccCCCcCCCCcceeeee
Confidence 4479999999998887743
No 119
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=30.28 E-value=40 Score=22.71 Aligned_cols=39 Identities=26% Similarity=0.524 Sum_probs=23.5
Q ss_pred cccccccCcceeecCCCCccchhHHHHHhhhhhhccCCccccccccc
Q 029136 11 DETEIDDDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLC 57 (198)
Q Consensus 11 de~e~ddd~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVC 57 (198)
+++-.....+..+.||.|+-++...- .. ++ .+...||.|
T Consensus 17 ~~v~~~s~~~v~W~C~~Cgh~w~~~v--~~-----R~-~~~~~CP~C 55 (55)
T PF14311_consen 17 SEVTPGSNKKVWWKCPKCGHEWKASV--ND-----RT-RRGKGCPYC 55 (55)
T ss_pred HHhCcCCCCEEEEECCCCCCeeEccH--hh-----hc-cCCCCCCCC
Confidence 33433445567899999976665431 11 11 556789988
No 120
>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=30.21 E-value=6 Score=24.99 Aligned_cols=11 Identities=18% Similarity=0.543 Sum_probs=4.1
Q ss_pred CCCCccchhHH
Q 029136 25 CPFCYLEIEAH 35 (198)
Q Consensus 25 CPfC~e~fD~~ 35 (198)
|++|++.+...
T Consensus 1 C~~C~~~~~~~ 11 (47)
T PF01844_consen 1 CQYCGKPGSDN 11 (47)
T ss_dssp -TTT--B--GG
T ss_pred CCCCCCcCccC
Confidence 78887765554
No 121
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=29.92 E-value=23 Score=34.62 Aligned_cols=42 Identities=24% Similarity=0.487 Sum_probs=26.3
Q ss_pred ceeecCCCCccchhHH--HHHhhhhhhccCCcccccccccccchhh
Q 029136 20 KACFPCPFCYLEIEAH--MICSHLQEEHCFEMKNAVCPLCAANLGK 63 (198)
Q Consensus 20 r~~F~CPfC~e~fD~~--~Lc~H~~eeH~~e~k~vVCPVCa~~v~~ 63 (198)
+...+||-|++.+.+. .|.- +++...+.---+||-|...+..
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 6789999998754443 3222 2222333444789999988763
No 122
>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=29.91 E-value=6.2 Score=29.41 Aligned_cols=55 Identities=27% Similarity=0.377 Sum_probs=24.5
Q ss_pred cCCCCccchhHHHHHhhhhhhccCCcccccccccccchh-------hhHhhhHhhhhhhhhhhhhc
Q 029136 24 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG-------KDAAEHFMVQHASSLKRRRK 82 (198)
Q Consensus 24 ~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~-------~d~v~Hit~qH~~~~Krrrr 82 (198)
.||-|..+++..+---||+.=+..=.+.+.||-|...+. .|+.= ||+|=||.|+|
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC----~~c~gLiSKkr 64 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFC----NHCHGLISKKR 64 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-TTT
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceee----ccCCceeecce
Confidence 466665555555522222222222245588999998753 35553 67777765544
No 123
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=29.72 E-value=12 Score=28.38 Aligned_cols=22 Identities=23% Similarity=0.384 Sum_probs=15.6
Q ss_pred ceeecCCCCcc-chhHHHHHhhh
Q 029136 20 KACFPCPFCYL-EIEAHMICSHL 41 (198)
Q Consensus 20 r~~F~CPfC~e-~fD~~~Lc~H~ 41 (198)
-..|.||+|.. .-.+..|..+.
T Consensus 19 f~d~~Cp~C~~~~~~~~~~~~~~ 41 (162)
T PF13462_consen 19 FFDFQCPHCAKFHEELEKLLKKY 41 (162)
T ss_dssp EE-TTSHHHHHHHHHHHHHHHHH
T ss_pred EECCCCHhHHHHHHHHhhhhhhc
Confidence 35799999976 66666777775
No 124
>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=29.38 E-value=19 Score=28.32 Aligned_cols=37 Identities=30% Similarity=0.549 Sum_probs=21.7
Q ss_pred cCCCCccchhH---HHHHhhhhhhccCCcccccccccccchhh
Q 029136 24 PCPFCYLEIEA---HMICSHLQEEHCFEMKNAVCPLCAANLGK 63 (198)
Q Consensus 24 ~CPfC~e~fD~---~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~ 63 (198)
.||||+....+ ..+.-|-.++++. .-+|+-|-+.||.
T Consensus 4 ~CpYCg~~~~l~~~~~iYg~~~~~~~~---~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 4 ICPYCGGPAELVDGSEIYGHRYDDGPY---LYVCTPCDAYVGC 43 (102)
T ss_pred ccCCCCCeeEEcccchhcCccCCCCce---eEECCCCCceeee
Confidence 69999763332 2233333222221 2689999999883
No 125
>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=29.30 E-value=38 Score=23.85 Aligned_cols=37 Identities=24% Similarity=0.584 Sum_probs=22.6
Q ss_pred eecCCCCccchhHHHHHhhhh------------------hhccCCccccccccccc
Q 029136 22 CFPCPFCYLEIEAHMICSHLQ------------------EEHCFEMKNAVCPLCAA 59 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~------------------eeH~~e~k~vVCPVCa~ 59 (198)
--.||+|...+|...|+.=.. +.|..| ...+||.|..
T Consensus 7 iL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~e-g~L~Cp~c~r 61 (68)
T PF03966_consen 7 ILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVE-GELICPECGR 61 (68)
T ss_dssp TBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTT-TEEEETTTTE
T ss_pred hhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccC-CEEEcCCCCC
Confidence 357999966887777766221 233333 5578999864
No 126
>PF14279 HNH_5: HNH endonuclease
Probab=29.28 E-value=26 Score=25.64 Aligned_cols=40 Identities=28% Similarity=0.659 Sum_probs=25.3
Q ss_pred CCCCccchhHHHHHhhhhhhccC--------CcccccccccccchhhhHhhhH
Q 029136 25 CPFCYLEIEAHMICSHLQEEHCF--------EMKNAVCPLCAANLGKDAAEHF 69 (198)
Q Consensus 25 CPfC~e~fD~~~Lc~H~~eeH~~--------e~k~vVCPVCa~~v~~d~v~Hi 69 (198)
|.||.++++....- +||=. ..+. ||-.|-...|...-.++
T Consensus 1 Ci~C~~~~~~~~~s----~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFS----EEHIIPESLGGKLKINN-VCDKCNNKFGSKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCC----ccccCchhcCCcccccc-hhHHHhHHHhHHHHHHH
Confidence 89998766554321 44533 3455 99999999886444444
No 127
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.11 E-value=31 Score=32.75 Aligned_cols=23 Identities=35% Similarity=0.912 Sum_probs=18.8
Q ss_pred eecCCCCccchhHHHHHhhhhhhc
Q 029136 22 CFPCPFCYLEIEAHMICSHLQEEH 45 (198)
Q Consensus 22 ~F~CPfC~e~fD~~~Lc~H~~eeH 45 (198)
+--||||.-.+...+.|.|++ .|
T Consensus 2 e~iCP~CkLsv~~~~m~~Hie-aH 24 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIE-AH 24 (393)
T ss_pred cccccceecccCHHHHHHHHH-hh
Confidence 356999977788889999998 44
No 128
>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=28.96 E-value=20 Score=27.78 Aligned_cols=17 Identities=29% Similarity=0.499 Sum_probs=11.7
Q ss_pred HHhcccccccchhhhhh
Q 029136 173 KLANKISVSSTMHFKID 189 (198)
Q Consensus 173 ~~~~~~~~~~~~~~~~~ 189 (198)
+++++..|.+|-.|+|+
T Consensus 134 ~~~~~~gi~gTPt~iIn 150 (178)
T cd03019 134 KLAKKYKITGVPAFVVN 150 (178)
T ss_pred HHHHHcCCCCCCeEEEC
Confidence 34566777777777775
No 129
>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=28.86 E-value=31 Score=23.82 Aligned_cols=13 Identities=31% Similarity=0.761 Sum_probs=9.2
Q ss_pred CcceeecCCCCcc
Q 029136 18 DVKACFPCPFCYL 30 (198)
Q Consensus 18 d~r~~F~CPfC~e 30 (198)
++-.+|.||-|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (50)
T cd00730 30 DLPDDWVCPVCGA 42 (50)
T ss_pred HCCCCCCCCCCCC
Confidence 4666788888854
No 130
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=28.83 E-value=27 Score=33.55 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=25.4
Q ss_pred eecCCCCccchh-HHHHHhhhhhhccCCccc
Q 029136 22 CFPCPFCYLEIE-AHMICSHLQEEHCFEMKN 51 (198)
Q Consensus 22 ~F~CPfC~e~fD-~~~Lc~H~~eeH~~e~k~ 51 (198)
...|=||..-.| .+.|..|+.+.|.+|-..
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 479999976555 899999999999998754
No 131
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.77 E-value=26 Score=33.39 Aligned_cols=44 Identities=23% Similarity=0.455 Sum_probs=28.1
Q ss_pred cCcceeecCCCCccchhHHH--HHhh-----hhhhccCCcccccccccccchh
Q 029136 17 DDVKACFPCPFCYLEIEAHM--ICSH-----LQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 17 dd~r~~F~CPfC~e~fD~~~--Lc~H-----~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
++++..|.||.|.+.|.... =|.| |..++-. ....||+|...++
T Consensus 21 ~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~--~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLS--NQPKCPLCRAEDQ 71 (397)
T ss_pred cccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHh--CCCCCCCCCCccc
Confidence 66788899999977654432 2333 4333322 2358999998765
No 132
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.76 E-value=40 Score=30.45 Aligned_cols=54 Identities=19% Similarity=0.349 Sum_probs=35.0
Q ss_pred eeecCCCC--ccchhHHHHHhhhhhhccCCcccccccccccc-hhh-hHhhhHhhhhhhhhh
Q 029136 21 ACFPCPFC--YLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN-LGK-DAAEHFMVQHASSLK 78 (198)
Q Consensus 21 ~~F~CPfC--~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~-v~~-d~v~Hit~qH~~~~K 78 (198)
..|.||-= .+-||--. | -|.|.....-.+|-+|..+ ++. =+-.||+-+|-.+|.
T Consensus 78 ~~~~cqvagc~~~~d~lD---~-~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fq 135 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALD---D-YEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQ 135 (253)
T ss_pred ccccccccchHHHHhhhh---h-HHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHH
Confidence 57999863 23333211 1 1345555556799999986 444 455799999999995
No 133
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=28.36 E-value=41 Score=28.82 Aligned_cols=30 Identities=27% Similarity=0.726 Sum_probs=22.0
Q ss_pred eeecCCCCcc--chhHHHHHhhhhhhccCCcccccccccccchh
Q 029136 21 ACFPCPFCYL--EIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 21 ~~F~CPfC~e--~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~ 62 (198)
..|.||-|.. .||.+-... -.||.|.+.+-
T Consensus 112 ~~y~C~~~~~r~sfdeA~~~~------------F~Cp~Cg~~L~ 143 (176)
T COG1675 112 NYYVCPNCHVKYSFDEAMELG------------FTCPKCGEDLE 143 (176)
T ss_pred CceeCCCCCCcccHHHHHHhC------------CCCCCCCchhh
Confidence 4699999954 777664332 68999998754
No 134
>PRK10220 hypothetical protein; Provisional
Probab=28.24 E-value=30 Score=27.95 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=7.9
Q ss_pred cccccccccccc
Q 029136 49 MKNAVCPLCAAN 60 (198)
Q Consensus 49 ~k~vVCPVCa~~ 60 (198)
....|||-|+--
T Consensus 18 ~~~~vCpeC~hE 29 (111)
T PRK10220 18 NGMYICPECAHE 29 (111)
T ss_pred CCeEECCcccCc
Confidence 345788888763
No 135
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.21 E-value=26 Score=27.36 Aligned_cols=36 Identities=17% Similarity=0.378 Sum_probs=21.1
Q ss_pred ceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccchhh
Q 029136 20 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 63 (198)
Q Consensus 20 r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~v~~ 63 (198)
-..|.||+|++ .-+. +.-.+ ---..+||+|-..-+.
T Consensus 19 pt~f~CP~Cge-~~v~-----v~~~k--~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGK-VSIS-----VKIKK--NIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCC-eEee-----eecCC--CcceEECCCCCCccCE
Confidence 35799999984 1111 11111 1234789999987554
No 136
>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=28.01 E-value=17 Score=24.44 Aligned_cols=10 Identities=50% Similarity=1.195 Sum_probs=8.0
Q ss_pred eeecCCCCcc
Q 029136 21 ACFPCPFCYL 30 (198)
Q Consensus 21 ~~F~CPfC~e 30 (198)
..|.||||+.
T Consensus 5 ~d~~Cp~C~~ 14 (98)
T cd02972 5 FDPLCPYCYL 14 (98)
T ss_pred ECCCCHhHHh
Confidence 4689999976
No 137
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=27.41 E-value=25 Score=34.22 Aligned_cols=17 Identities=35% Similarity=0.673 Sum_probs=14.2
Q ss_pred cCCcccccccccccchh
Q 029136 46 CFEMKNAVCPLCAANLG 62 (198)
Q Consensus 46 ~~e~k~vVCPVCa~~v~ 62 (198)
-.+++.-|||||...||
T Consensus 32 ~~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 32 GAEPNTNVCPVCLGLPG 48 (474)
T ss_pred CCCCCCCcCccccCCCC
Confidence 34577899999999987
No 138
>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=27.06 E-value=9 Score=23.74 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=5.2
Q ss_pred ccccccccc
Q 029136 49 MKNAVCPLC 57 (198)
Q Consensus 49 ~k~vVCPVC 57 (198)
.....||+|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 444557766
No 139
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.51 E-value=16 Score=28.52 Aligned_cols=35 Identities=26% Similarity=0.485 Sum_probs=21.0
Q ss_pred cccCcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 15 IDDDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 15 ~ddd~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
.|...++.+.||+|+.. -+ -+.-+.--.|.-|-..
T Consensus 28 ie~~~~~~~~Cp~C~~~-~V----------kR~a~GIW~C~kCg~~ 62 (89)
T COG1997 28 IEAQQRAKHVCPFCGRT-TV----------KRIATGIWKCRKCGAK 62 (89)
T ss_pred HHHHHhcCCcCCCCCCc-ce----------eeeccCeEEcCCCCCe
Confidence 34567889999999763 11 1222334557777655
No 140
>PF14353 CpXC: CpXC protein
Probab=26.49 E-value=31 Score=26.65 Aligned_cols=14 Identities=29% Similarity=0.671 Sum_probs=10.6
Q ss_pred eeecCCCCccchhH
Q 029136 21 ACFPCPFCYLEIEA 34 (198)
Q Consensus 21 ~~F~CPfC~e~fD~ 34 (198)
..|.||.|+..+-+
T Consensus 37 ~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 37 FSFTCPSCGHKFRL 50 (128)
T ss_pred CEEECCCCCCceec
Confidence 37999999885543
No 141
>PF14828 Amnionless: Amnionless
Probab=25.54 E-value=32 Score=32.92 Aligned_cols=42 Identities=29% Similarity=0.657 Sum_probs=26.4
Q ss_pred cCCCCccchhHHHHHhhh----hhhccCCccc---ccccccccchhhhHh
Q 029136 24 PCPFCYLEIEAHMICSHL----QEEHCFEMKN---AVCPLCAANLGKDAA 66 (198)
Q Consensus 24 ~CPfC~e~fD~~~Lc~H~----~eeH~~e~k~---vVCPVCa~~v~~d~v 66 (198)
-|+ |+.+.-+..+|..+ ..-||..+=. --||||.+++....-
T Consensus 193 gC~-C~n~~~l~~ICs~v~~~C~~~~C~~pl~P~GhCC~iCGa~v~~~~~ 241 (437)
T PF14828_consen 193 GCP-CGNDEVLEWICSNVLQRCPKPHCRSPLRPEGHCCPICGAIVTLEYS 241 (437)
T ss_pred cCc-cCcccchhhhhHHhhCcCCCCccCCCCCCCCCchhhcceEEEEeec
Confidence 344 66666667777655 4556655422 349999999774433
No 142
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=25.51 E-value=12 Score=29.50 Aligned_cols=20 Identities=30% Similarity=0.638 Sum_probs=12.6
Q ss_pred cceeecCCCCcc-chhHHHHH
Q 029136 19 VKACFPCPFCYL-EIEAHMIC 38 (198)
Q Consensus 19 ~r~~F~CPfC~e-~fD~~~Lc 38 (198)
+-..|.||||+- .--+..|.
T Consensus 4 ~~~D~~Cp~cy~~~~~l~~l~ 24 (193)
T PF01323_consen 4 FFFDFICPWCYLASPRLRKLR 24 (193)
T ss_dssp EEEBTTBHHHHHHHHHHHHHH
T ss_pred EEEeCCCHHHHHHHHHHHHHH
Confidence 345799999975 43444444
No 143
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=25.24 E-value=21 Score=27.89 Aligned_cols=11 Identities=36% Similarity=0.899 Sum_probs=9.4
Q ss_pred ceeecCCCCcc
Q 029136 20 KACFPCPFCYL 30 (198)
Q Consensus 20 r~~F~CPfC~e 30 (198)
.+.|.|+||+.
T Consensus 34 haky~CsfCGK 44 (92)
T KOG0402|consen 34 HAKYTCSFCGK 44 (92)
T ss_pred hhhhhhhhcch
Confidence 46899999986
No 144
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=25.15 E-value=41 Score=21.37 Aligned_cols=31 Identities=19% Similarity=0.490 Sum_probs=18.4
Q ss_pred ecCCCCccchhHHHHHhhhhhhccCCccccccccccc
Q 029136 23 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 59 (198)
Q Consensus 23 F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~ 59 (198)
..||-|...|++.. +.=+...+.+-||-|..
T Consensus 3 i~CP~C~~~f~v~~------~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPD------DKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCH------HHcccCCcEEECCCCCc
Confidence 46888876555442 11134455677888864
No 145
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.92 E-value=33 Score=25.18 Aligned_cols=13 Identities=31% Similarity=0.938 Sum_probs=9.1
Q ss_pred Ccccccccccccc
Q 029136 48 EMKNAVCPLCAAN 60 (198)
Q Consensus 48 e~k~vVCPVCa~~ 60 (198)
+.+.++||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 5566788888764
No 146
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=24.75 E-value=48 Score=33.78 Aligned_cols=54 Identities=28% Similarity=0.508 Sum_probs=33.4
Q ss_pred ccCcceeecCCCCcc-chh-HHHHHhh-----hhh---hccCCcccccccccccchhhhHhhhH
Q 029136 16 DDDVKACFPCPFCYL-EIE-AHMICSH-----LQE---EHCFEMKNAVCPLCAANLGKDAAEHF 69 (198)
Q Consensus 16 ddd~r~~F~CPfC~e-~fD-~~~Lc~H-----~~e---eH~~e~k~vVCPVCa~~v~~d~v~Hi 69 (198)
+||-..+-.|-+|.+ -=| ++.=|.| |.. +--.+..|+.||+|.-..+-|+.+|-
T Consensus 530 ~~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred CccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 345556678999943 222 2222333 322 33457788999999998887766554
No 147
>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=23.79 E-value=58 Score=19.27 Aligned_cols=20 Identities=25% Similarity=0.644 Sum_probs=10.6
Q ss_pred ecCCCCccchh-HHHHHhhhh
Q 029136 23 FPCPFCYLEIE-AHMICSHLQ 42 (198)
Q Consensus 23 F~CPfC~e~fD-~~~Lc~H~~ 42 (198)
|.|..|...|. ...+-.|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 55666655444 445555543
No 148
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=23.62 E-value=23 Score=26.27 Aligned_cols=34 Identities=21% Similarity=0.245 Sum_probs=21.3
Q ss_pred hhHHhhhHHHHHHHhcccccccchhhhhhhheeeec
Q 029136 161 EYKLLWSQLLFKKLANKISVSSTMHFKIDVLLVIGI 196 (198)
Q Consensus 161 ~~k~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (198)
.++..+.+.. +++++..|.+|=.|+++--++-|.
T Consensus 110 ~~~~~~~~~~--~~~~~~gi~gtPt~~v~g~~~~G~ 143 (154)
T cd03023 110 EIEATIDKNR--QLARALGITGTPAFIIGDTVIPGA 143 (154)
T ss_pred HHHHHHHHHH--HHHHHcCCCcCCeEEECCEEecCC
Confidence 4454444433 566777888888888775555553
No 149
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=23.14 E-value=56 Score=24.66 Aligned_cols=31 Identities=16% Similarity=0.317 Sum_probs=25.3
Q ss_pred cCCcccccccccccchh-hhHhhhHhhhhhhh
Q 029136 46 CFEMKNAVCPLCAANLG-KDAAEHFMVQHASS 76 (198)
Q Consensus 46 ~~e~k~vVCPVCa~~v~-~d~v~Hit~qH~~~ 76 (198)
.-+.+-.||-.|...|+ ..+.+|++..|..+
T Consensus 6 ~~~~~vlIC~~C~~av~~~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 6 NPEYRVLICRQCQYAVQPSEVESHLRKRHHIL 37 (109)
T ss_pred cCcCCEEEeCCCCcccCchHHHHHHHHhcccc
Confidence 34567799999998876 79999998878776
No 150
>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=22.98 E-value=17 Score=27.87 Aligned_cols=38 Identities=24% Similarity=0.563 Sum_probs=12.3
Q ss_pred cCCCCccchhHHHHH-hhhhhhccC-----------Ccccccccccccch
Q 029136 24 PCPFCYLEIEAHMIC-SHLQEEHCF-----------EMKNAVCPLCAANL 61 (198)
Q Consensus 24 ~CPfC~e~fD~~~Lc-~H~~eeH~~-----------e~k~vVCPVCa~~v 61 (198)
.||+|.+.++...+- .=|..-|-+ +++.-+|++|..+.
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 599998877655542 447777765 55667899998763
No 151
>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=22.85 E-value=29 Score=26.56 Aligned_cols=8 Identities=50% Similarity=1.364 Sum_probs=6.2
Q ss_pred ecCCCCcc
Q 029136 23 FPCPFCYL 30 (198)
Q Consensus 23 F~CPfC~e 30 (198)
.+||||++
T Consensus 2 I~CP~CG~ 9 (84)
T PF04267_consen 2 IPCPHCGP 9 (84)
T ss_dssp EEETTTEE
T ss_pred ccCCCCCc
Confidence 47899976
No 152
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=22.44 E-value=30 Score=23.02 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=7.9
Q ss_pred eecCCCCccc
Q 029136 22 CFPCPFCYLE 31 (198)
Q Consensus 22 ~F~CPfC~e~ 31 (198)
.-.||||+.-
T Consensus 29 ~~~CpYCg~~ 38 (40)
T PF10276_consen 29 PVVCPYCGTR 38 (40)
T ss_dssp EEEETTTTEE
T ss_pred eEECCCCCCE
Confidence 5789999753
No 153
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=22.40 E-value=34 Score=33.97 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=16.2
Q ss_pred hhccCCcccccccccccchh
Q 029136 43 EEHCFEMKNAVCPLCAANLG 62 (198)
Q Consensus 43 eeH~~e~k~vVCPVCa~~v~ 62 (198)
.+.-.+++.-|||||...||
T Consensus 85 ~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 85 YNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred cccCCCCccCcCccccCCCC
Confidence 34445788899999999988
No 154
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=22.33 E-value=42 Score=32.11 Aligned_cols=41 Identities=20% Similarity=0.386 Sum_probs=30.9
Q ss_pred eeecCCC--Ccc-chhHHHHHhhhhhhccC-----------------Ccccccccccccch
Q 029136 21 ACFPCPF--CYL-EIEAHMICSHLQEEHCF-----------------EMKNAVCPLCAANL 61 (198)
Q Consensus 21 ~~F~CPf--C~e-~fD~~~Lc~H~~eeH~~-----------------e~k~vVCPVCa~~v 61 (198)
--|.||. |.+ .-.+-+|--|.-.-|+. +.|+-+|+||..+-
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhh
Confidence 3488986 755 66788999999888832 34677899999874
No 155
>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=21.56 E-value=33 Score=31.50 Aligned_cols=20 Identities=35% Similarity=0.632 Sum_probs=13.7
Q ss_pred hccCCcccccccccccchhh
Q 029136 44 EHCFEMKNAVCPLCAANLGK 63 (198)
Q Consensus 44 eH~~e~k~vVCPVCa~~v~~ 63 (198)
+...+++.-|||+|...||.
T Consensus 25 ~~~~~pNt~v~~~~lg~PGt 44 (289)
T PF02934_consen 25 EFGAEPNTNVCPVCLGLPGT 44 (289)
T ss_dssp STTSCTTSSB-TTTTT-TTC
T ss_pred CCCCCCccccCceeccCCCC
Confidence 33346888999999999883
No 156
>PF10265 DUF2217: Uncharacterized conserved protein (DUF2217); InterPro: IPR019392 This is a family of conserved proteins varying in length from 500-600 residues. Their function is not known.
Probab=21.38 E-value=1.5e+02 Score=29.59 Aligned_cols=12 Identities=58% Similarity=0.628 Sum_probs=8.1
Q ss_pred hhhhhhhhcccC
Q 029136 74 ASSLKRRRKCLK 85 (198)
Q Consensus 74 ~~~~Krrrr~rk 85 (198)
.|.|||||++||
T Consensus 32 A~~lkRRr~kkk 43 (514)
T PF10265_consen 32 AHYLKRRRRKKK 43 (514)
T ss_pred HHHHHHhhcccc
Confidence 344888777666
No 157
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=21.21 E-value=42 Score=28.54 Aligned_cols=12 Identities=42% Similarity=0.985 Sum_probs=8.3
Q ss_pred cccccccccccc
Q 029136 49 MKNAVCPLCAAN 60 (198)
Q Consensus 49 ~k~vVCPVCa~~ 60 (198)
..+.+||||-+.
T Consensus 147 e~P~~CPiCga~ 158 (166)
T COG1592 147 EAPEVCPICGAP 158 (166)
T ss_pred CCCCcCCCCCCh
Confidence 345788888764
No 158
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.18 E-value=38 Score=26.61 Aligned_cols=32 Identities=22% Similarity=0.461 Sum_probs=20.7
Q ss_pred cCcceeecCCCCccchhHHHHHhhhhhhccCCcccccccccccc
Q 029136 17 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 60 (198)
Q Consensus 17 dd~r~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 60 (198)
++....+.|+-|+..+..... ....||-|...
T Consensus 66 e~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 66 VDEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred EecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 345678899999866554321 22459999874
No 159
>PF14968 CCDC84: Coiled coil protein 84
Probab=21.18 E-value=48 Score=31.05 Aligned_cols=20 Identities=35% Similarity=0.732 Sum_probs=15.2
Q ss_pred ccCcceeecCCCCccchhHH
Q 029136 16 DDDVKACFPCPFCYLEIEAH 35 (198)
Q Consensus 16 ddd~r~~F~CPfC~e~fD~~ 35 (198)
|.+-+..|=|+||+.+++..
T Consensus 52 ~~~~~~~fWC~fC~~ev~~~ 71 (336)
T PF14968_consen 52 DPEHRNRFWCVFCDCEVREH 71 (336)
T ss_pred CccccceeEeeCccchhhhc
Confidence 34567889999998877754
No 160
>TIGR00165 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.
Probab=21.01 E-value=53 Score=24.24 Aligned_cols=30 Identities=17% Similarity=0.357 Sum_probs=18.8
Q ss_pred cccccccccccchh------hhHhhhHhhhhhhhhh
Q 029136 49 MKNAVCPLCAANLG------KDAAEHFMVQHASSLK 78 (198)
Q Consensus 49 ~k~vVCPVCa~~v~------~d~v~Hit~qH~~~~K 78 (198)
.+.-+||+|+..+. .+++..+.+.+|-++-
T Consensus 3 ~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~GkIlp 38 (70)
T TIGR00165 3 RRKKYCRFTAEGIQFIDYKDLDLLKKFISERGKILP 38 (70)
T ss_pred CCCCCCCccCCCCCcCCccCHHHHHHhcCCCCeEcC
Confidence 34567888876532 3566666666666653
No 161
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.77 E-value=25 Score=32.62 Aligned_cols=41 Identities=29% Similarity=0.646 Sum_probs=24.0
Q ss_pred eeecCCCCcc--chhHHHH-HhhhhhhccCCccc-----ccccccccch
Q 029136 21 ACFPCPFCYL--EIEAHMI-CSHLQEEHCFEMKN-----AVCPLCAANL 61 (198)
Q Consensus 21 ~~F~CPfC~e--~fD~~~L-c~H~~eeH~~e~k~-----vVCPVCa~~v 61 (198)
.+-.||+|++ -+--+.. |.|+-=--|.-++. -.||-|.+.+
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 4568999987 3333444 77754333433332 2688887764
No 162
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=20.69 E-value=74 Score=24.58 Aligned_cols=37 Identities=30% Similarity=0.682 Sum_probs=26.8
Q ss_pred eecCCCCcc-----chhHHHHHhhhhhhccC------Cccccccccccc
Q 029136 22 CFPCPFCYL-----EIEAHMICSHLQEEHCF------EMKNAVCPLCAA 59 (198)
Q Consensus 22 ~F~CPfC~e-----~fD~~~Lc~H~~eeH~~------e~k~vVCPVCa~ 59 (198)
+=.||-|-. .+ +-++|.|+--.|+. ..+.+-||+|..
T Consensus 31 dg~Cp~Ck~PgDdCPL-v~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq 78 (84)
T KOG1493|consen 31 DGCCPDCKLPGDDCPL-VWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQ 78 (84)
T ss_pred CCcCCCCcCCCCCCcc-HHHHHHHHHHHHHHHHHhcCccccccCCcchh
Confidence 346888832 34 67899999888875 445689999964
No 163
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=20.67 E-value=45 Score=23.09 Aligned_cols=32 Identities=25% Similarity=0.636 Sum_probs=11.7
Q ss_pred eeecCCCCccchhHHHHHhhhhhhccCCccccccccccc
Q 029136 21 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 59 (198)
Q Consensus 21 ~~F~CPfC~e~fD~~~Lc~H~~eeH~~e~k~vVCPVCa~ 59 (198)
.-+||| |+..+=+- ...++.+ ..++.||-|..
T Consensus 14 ~~~PC~-Cgf~IC~~-C~~~i~~-----~~~g~CPgCr~ 45 (48)
T PF14570_consen 14 DFYPCE-CGFQICRF-CYHDILE-----NEGGRCPGCRE 45 (48)
T ss_dssp T--SST-TS----HH-HHHHHTT-----SS-SB-TTT--
T ss_pred ccccCc-CCCcHHHH-HHHHHHh-----ccCCCCCCCCC
Confidence 457887 75433111 1122222 35799999964
No 164
>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=20.36 E-value=34 Score=29.20 Aligned_cols=20 Identities=20% Similarity=0.634 Sum_probs=0.0
Q ss_pred ccccccccchh-hhHhhhHhh
Q 029136 52 AVCPLCAANLG-KDAAEHFMV 71 (198)
Q Consensus 52 vVCPVCa~~v~-~d~v~Hit~ 71 (198)
.+||||..+|- ..|-.||+.
T Consensus 169 ~~cPitGe~IP~~e~~eHmRi 189 (229)
T PF12230_consen 169 IICPITGEMIPADEMDEHMRI 189 (229)
T ss_dssp ---------------------
T ss_pred ccccccccccccccccccccc
Confidence 47888888855 578888854
No 165
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.30 E-value=57 Score=30.88 Aligned_cols=29 Identities=24% Similarity=0.496 Sum_probs=22.7
Q ss_pred ccccccCcceeecCCCCccchhHHHHHhh
Q 029136 12 ETEIDDDVKACFPCPFCYLEIEAHMICSH 40 (198)
Q Consensus 12 e~e~ddd~r~~F~CPfC~e~fD~~~Lc~H 40 (198)
+.+.-+-+..+|+||-|...|-..+|-.|
T Consensus 10 ~~~~~~q~~~~fpc~ic~r~f~~~~L~kh 38 (351)
T KOG3940|consen 10 KTSRLAQMQMRFPCRICQREFRRRELMKH 38 (351)
T ss_pred cccccccccccccccccccchhhhhhhcc
Confidence 33444667889999999988888888766
Done!