Query 028989
Match_columns 200
No_of_seqs 142 out of 169
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 05:43:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028989.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028989hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05605 zf-Di19: Drought indu 99.8 2.9E-20 6.3E-25 127.5 4.1 54 43-96 1-54 (54)
2 PF14571 Di19_C: Stress-induce 99.8 4.1E-20 8.9E-25 143.6 3.8 59 115-173 1-60 (105)
3 KOG1280 Uncharacterized conser 99.0 2.8E-10 6E-15 104.6 5.1 122 21-149 60-201 (381)
4 PF13894 zf-C2H2_4: C2H2-type 94.8 0.025 5.4E-07 31.0 2.0 23 45-67 1-24 (24)
5 COG5236 Uncharacterized conser 94.6 0.054 1.2E-06 51.3 4.9 52 44-101 220-311 (493)
6 KOG2923 Uncharacterized conser 94.1 0.023 4.9E-07 41.7 1.0 45 31-84 8-55 (67)
7 COG5216 Uncharacterized conser 94.0 0.015 3.3E-07 42.2 -0.0 37 39-84 17-55 (67)
8 KOG2462 C2H2-type Zn-finger pr 93.0 0.064 1.4E-06 48.7 2.3 37 42-82 159-196 (279)
9 PHA00732 hypothetical protein 92.7 0.12 2.5E-06 38.5 3.0 42 45-91 2-44 (79)
10 PF00096 zf-C2H2: Zinc finger, 92.3 0.077 1.7E-06 29.6 1.2 21 45-65 1-22 (23)
11 PF12756 zf-C2H2_2: C2H2 type 92.0 0.081 1.8E-06 37.8 1.4 48 46-93 1-72 (100)
12 PLN03086 PRLI-interacting fact 91.6 0.17 3.8E-06 49.9 3.6 45 43-92 452-497 (567)
13 PF13913 zf-C2HC_2: zinc-finge 91.5 0.15 3.3E-06 30.2 1.9 21 44-64 2-22 (25)
14 PF09237 GAGA: GAGA factor; I 90.9 0.16 3.5E-06 35.9 1.8 26 72-97 23-50 (54)
15 PF13909 zf-H2C2_5: C2H2-type 90.2 0.19 4.2E-06 28.5 1.5 24 45-68 1-24 (24)
16 smart00531 TFIIE Transcription 89.9 0.28 6.1E-06 39.6 2.8 41 39-84 94-134 (147)
17 PHA00733 hypothetical protein 87.5 0.72 1.6E-05 36.9 3.6 50 43-96 72-124 (128)
18 KOG2462 C2H2-type Zn-finger pr 87.2 0.48 1E-05 43.2 2.7 47 44-92 187-236 (279)
19 PHA02768 hypothetical protein; 86.9 0.57 1.2E-05 33.2 2.4 34 44-81 5-39 (55)
20 smart00834 CxxC_CXXC_SSSS Puta 86.7 0.27 5.8E-06 31.0 0.6 33 43-83 4-36 (41)
21 KOG1842 FYVE finger-containing 84.8 0.57 1.2E-05 45.5 2.0 36 38-73 9-45 (505)
22 TIGR01206 lysW lysine biosynth 84.8 0.31 6.7E-06 34.2 0.2 30 44-82 2-31 (54)
23 PLN03086 PRLI-interacting fact 84.6 0.94 2E-05 44.9 3.4 39 43-84 477-515 (567)
24 TIGR02098 MJ0042_CXXC MJ0042 f 84.6 0.61 1.3E-05 29.3 1.4 33 45-83 3-35 (38)
25 smart00504 Ubox Modified RING 83.4 1.2 2.6E-05 29.9 2.7 29 50-85 19-47 (63)
26 PRK09710 lar restriction allev 83.4 0.42 9.1E-06 34.9 0.4 31 45-84 7-38 (64)
27 PF08271 TF_Zn_Ribbon: TFIIB z 83.0 0.41 8.9E-06 31.2 0.2 35 45-89 1-35 (43)
28 PF12756 zf-C2H2_2: C2H2 type 81.2 1.2 2.6E-05 31.7 2.1 26 43-68 49-75 (100)
29 PF02176 zf-TRAF: TRAF-type zi 81.2 0.8 1.7E-05 30.8 1.1 45 44-90 9-60 (60)
30 TIGR02605 CxxC_CxxC_SSSS putat 80.3 1.1 2.4E-05 29.8 1.5 32 43-82 4-35 (52)
31 cd00350 rubredoxin_like Rubred 79.8 0.93 2E-05 28.3 1.0 25 45-82 2-26 (33)
32 PF09986 DUF2225: Uncharacteri 78.3 0.63 1.4E-05 40.0 -0.2 49 44-92 5-67 (214)
33 PF13912 zf-C2H2_6: C2H2-type 78.1 1.7 3.7E-05 24.9 1.7 24 45-68 2-26 (27)
34 PF08274 PhnA_Zn_Ribbon: PhnA 77.8 0.79 1.7E-05 28.7 0.2 24 46-81 4-27 (30)
35 PLN03208 E3 ubiquitin-protein 76.8 1.1 2.4E-05 38.8 0.9 49 40-88 14-83 (193)
36 PRK14890 putative Zn-ribbon RN 76.6 2.1 4.7E-05 30.8 2.2 34 40-80 21-55 (59)
37 smart00734 ZnF_Rad18 Rad18-lik 76.1 2.1 4.6E-05 25.6 1.8 19 46-64 3-21 (26)
38 KOG3623 Homeobox transcription 75.8 1.2 2.7E-05 45.7 1.1 51 42-92 208-261 (1007)
39 PRK14892 putative transcriptio 75.4 0.93 2E-05 35.4 0.1 37 41-86 18-55 (99)
40 cd00729 rubredoxin_SM Rubredox 74.9 1.6 3.5E-05 27.6 1.1 26 44-82 2-27 (34)
41 PF03145 Sina: Seven in absent 74.7 2.6 5.6E-05 35.2 2.5 54 43-99 13-75 (198)
42 PHA00616 hypothetical protein 74.7 2 4.3E-05 29.2 1.5 25 45-69 2-27 (44)
43 TIGR00373 conserved hypothetic 73.2 3.1 6.6E-05 34.3 2.6 36 39-84 104-139 (158)
44 PRK06266 transcription initiat 72.9 3.1 6.6E-05 35.1 2.6 36 39-84 112-147 (178)
45 PRK00398 rpoP DNA-directed RNA 72.9 2.5 5.4E-05 27.8 1.6 29 44-83 3-31 (46)
46 PF04780 DUF629: Protein of un 71.3 3.2 6.8E-05 40.4 2.6 41 42-82 55-99 (466)
47 PF14354 Lar_restr_allev: Rest 71.2 1.8 3.9E-05 29.5 0.7 31 44-81 3-37 (61)
48 smart00355 ZnF_C2H2 zinc finge 70.2 4.4 9.6E-05 21.7 2.1 20 45-64 1-21 (26)
49 PF14255 Cys_rich_CPXG: Cystei 68.8 1.7 3.7E-05 30.3 0.2 32 45-83 1-34 (52)
50 PF09723 Zn-ribbon_8: Zinc rib 66.9 1.3 2.8E-05 29.0 -0.7 31 43-81 4-34 (42)
51 PF14206 Cys_rich_CPCC: Cystei 66.5 2.7 5.8E-05 31.6 0.8 27 44-81 1-28 (78)
52 PF04564 U-box: U-box domain; 66.4 8.7 0.00019 27.4 3.4 38 42-85 2-51 (73)
53 PF05129 Elf1: Transcription e 66.0 2.4 5.2E-05 31.7 0.5 35 42-83 20-56 (81)
54 PF12773 DZR: Double zinc ribb 65.4 3.7 7.9E-05 27.0 1.2 28 46-85 14-41 (50)
55 PF05605 zf-Di19: Drought indu 64.1 5.2 0.00011 27.0 1.8 24 44-68 31-54 (54)
56 PTZ00255 60S ribosomal protein 64.1 1.8 3.9E-05 33.5 -0.5 16 38-53 30-45 (90)
57 PF08996 zf-DNA_Pol: DNA Polym 63.9 1.5 3.3E-05 36.9 -1.1 56 42-99 16-72 (188)
58 TIGR03655 anti_R_Lar restricti 63.4 3.1 6.7E-05 28.3 0.6 8 46-53 3-10 (53)
59 PF07282 OrfB_Zn_ribbon: Putat 61.5 6.8 0.00015 27.2 2.1 42 40-92 24-65 (69)
60 PF07191 zinc-ribbons_6: zinc- 60.9 0.68 1.5E-05 34.3 -3.2 53 46-102 3-62 (70)
61 KOG0320 Predicted E3 ubiquitin 60.1 6.1 0.00013 34.3 1.9 43 43-87 130-181 (187)
62 PF12171 zf-C2H2_jaz: Zinc-fin 58.7 6.4 0.00014 22.9 1.3 21 45-65 2-23 (27)
63 TIGR00280 L37a ribosomal prote 57.8 4.2 9.1E-05 31.5 0.5 16 38-53 29-44 (91)
64 PRK03976 rpl37ae 50S ribosomal 57.4 4.4 9.5E-05 31.3 0.6 16 38-53 30-45 (90)
65 PF03470 zf-XS: XS zinc finger 56.6 7.3 0.00016 26.4 1.5 23 76-98 1-23 (43)
66 COG2888 Predicted Zn-ribbon RN 56.0 11 0.00024 27.3 2.4 35 39-80 22-57 (61)
67 COG0675 Transposase and inacti 54.8 7.3 0.00016 33.0 1.6 48 31-94 296-343 (364)
68 PF11793 FANCL_C: FANCL C-term 54.8 8.1 0.00017 27.8 1.6 48 39-86 15-68 (70)
69 PRK12496 hypothetical protein; 54.6 7.7 0.00017 32.2 1.6 28 44-84 127-154 (164)
70 PF07754 DUF1610: Domain of un 53.8 7.6 0.00017 23.3 1.1 13 40-52 12-24 (24)
71 smart00659 RPOLCX RNA polymera 53.0 9 0.0002 25.6 1.5 28 44-83 2-29 (44)
72 COG5175 MOT2 Transcriptional r 52.0 6.5 0.00014 37.6 0.8 21 59-84 44-64 (480)
73 PF04423 Rad50_zn_hook: Rad50 51.8 8.4 0.00018 26.0 1.2 19 74-92 21-43 (54)
74 COG4888 Uncharacterized Zn rib 51.4 7.4 0.00016 30.9 1.0 36 42-82 20-55 (104)
75 TIGR00100 hypA hydrogenase nic 51.0 6.2 0.00013 30.9 0.5 30 40-82 66-95 (115)
76 PRK12495 hypothetical protein; 50.9 8.8 0.00019 34.2 1.5 31 42-85 40-70 (226)
77 KOG2593 Transcription initiati 50.8 7.1 0.00015 37.8 0.9 61 32-99 116-190 (436)
78 PF08209 Sgf11: Sgf11 (transcr 50.5 11 0.00024 24.1 1.5 18 74-91 5-23 (33)
79 PF13395 HNH_4: HNH endonuclea 50.3 8.1 0.00017 26.2 0.9 13 47-59 1-13 (54)
80 PF01780 Ribosomal_L37ae: Ribo 50.2 5.3 0.00011 30.9 -0.0 15 39-53 30-44 (90)
81 PF15616 TerY-C: TerY-C metal 49.9 4.8 0.0001 33.0 -0.3 43 44-88 77-120 (131)
82 PF13248 zf-ribbon_3: zinc-rib 49.9 9.8 0.00021 22.4 1.1 9 46-54 4-12 (26)
83 PF11672 DUF3268: Protein of u 49.7 7.4 0.00016 30.6 0.7 37 46-85 4-43 (102)
84 PF13465 zf-H2C2_2: Zinc-finge 49.7 11 0.00023 22.1 1.3 22 59-82 2-23 (26)
85 PF14616 DUF4451: Domain of un 49.0 10 0.00023 30.2 1.5 28 73-100 25-57 (124)
86 PF10571 UPF0547: Uncharacteri 48.8 10 0.00022 22.9 1.1 9 46-54 2-10 (26)
87 COG4049 Uncharacterized protei 48.4 5.9 0.00013 28.8 0.0 26 75-100 19-46 (65)
88 PF02146 SIR2: Sir2 family; I 47.5 15 0.00032 30.0 2.2 41 43-88 104-144 (178)
89 PF14279 HNH_5: HNH endonuclea 47.4 6.6 0.00014 28.7 0.1 44 47-91 1-48 (71)
90 TIGR00686 phnA alkylphosphonat 46.4 8.6 0.00019 30.8 0.6 25 46-82 4-28 (109)
91 COG1592 Rubrerythrin [Energy p 46.3 13 0.00027 31.6 1.7 25 44-82 134-158 (166)
92 smart00661 RPOL9 RNA polymeras 45.8 8.8 0.00019 25.1 0.5 28 46-82 2-29 (52)
93 KOG2231 Predicted E3 ubiquitin 45.7 13 0.00029 37.7 2.0 29 42-70 180-209 (669)
94 PF13240 zinc_ribbon_2: zinc-r 45.5 7 0.00015 22.8 0.0 7 47-53 2-8 (23)
95 PRK00464 nrdR transcriptional 44.5 12 0.00026 31.2 1.3 33 46-84 2-39 (154)
96 PF14634 zf-RING_5: zinc-RING 43.6 18 0.0004 23.2 1.8 10 71-80 34-43 (44)
97 PF01155 HypA: Hydrogenase exp 42.9 7.5 0.00016 30.3 -0.2 30 40-82 66-95 (113)
98 COG5189 SFP1 Putative transcri 42.7 13 0.00029 35.2 1.4 40 44-83 349-408 (423)
99 smart00451 ZnF_U1 U1-like zinc 42.5 19 0.00041 21.5 1.6 21 44-64 3-24 (35)
100 PRK12380 hydrogenase nickel in 41.8 11 0.00024 29.5 0.6 30 40-82 66-95 (113)
101 KOG0402 60S ribosomal protein 40.2 8.2 0.00018 29.9 -0.3 15 39-53 31-45 (92)
102 PF05207 zf-CSL: CSL zinc fing 40.1 12 0.00026 25.9 0.5 45 32-85 5-52 (55)
103 cd00730 rubredoxin Rubredoxin; 40.1 17 0.00036 25.0 1.2 14 40-53 30-43 (50)
104 COG4311 SoxD Sarcosine oxidase 39.9 13 0.00028 29.3 0.7 9 44-52 3-11 (97)
105 PRK03922 hypothetical protein; 39.8 13 0.00029 29.9 0.8 16 44-59 49-64 (113)
106 PF02892 zf-BED: BED zinc fing 39.6 16 0.00035 23.2 1.0 27 42-68 14-45 (45)
107 PRK03824 hypA hydrogenase nick 39.5 15 0.00033 29.6 1.1 18 40-57 66-83 (135)
108 smart00507 HNHc HNH nucleases. 39.3 5.8 0.00013 24.6 -1.1 21 45-65 11-31 (52)
109 PF04475 DUF555: Protein of un 38.8 14 0.0003 29.3 0.8 16 44-59 47-62 (102)
110 PF04780 DUF629: Protein of un 38.7 15 0.00033 35.8 1.1 29 72-100 56-86 (466)
111 KOG2177 Predicted E3 ubiquitin 38.2 14 0.0003 29.6 0.7 37 42-80 11-54 (386)
112 PRK11595 DNA utilization prote 37.7 19 0.00041 30.8 1.4 34 46-81 7-42 (227)
113 COG1499 NMD3 NMD protein affec 37.6 19 0.0004 33.9 1.5 40 43-82 5-52 (355)
114 PF12230 PRP21_like_P: Pre-mRN 37.4 11 0.00024 32.3 0.0 21 74-94 169-190 (229)
115 PF12874 zf-met: Zinc-finger o 36.9 26 0.00057 19.4 1.5 20 45-64 1-21 (25)
116 smart00614 ZnF_BED BED zinc fi 35.9 24 0.00052 23.4 1.5 27 43-69 17-49 (50)
117 PRK00420 hypothetical protein; 35.9 24 0.00052 28.2 1.7 27 45-83 24-50 (112)
118 PF12230 PRP21_like_P: Pre-mRN 35.6 12 0.00027 32.0 0.0 23 44-66 168-190 (229)
119 KOG1002 Nucleotide excision re 35.5 25 0.00055 35.6 2.1 54 38-91 530-593 (791)
120 TIGR00570 cdk7 CDK-activating 35.4 19 0.00041 33.4 1.1 37 45-82 4-52 (309)
121 PF05876 Terminase_GpA: Phage 34.8 17 0.00037 35.5 0.9 43 42-86 198-242 (557)
122 KOG3623 Homeobox transcription 34.1 23 0.0005 37.0 1.6 52 40-93 277-331 (1007)
123 TIGR02300 FYDLN_acid conserved 34.0 25 0.00055 28.9 1.6 34 40-86 5-39 (129)
124 KOG4696 Uncharacterized conser 33.6 24 0.00051 33.4 1.5 21 45-65 3-23 (393)
125 KOG3576 Ovo and related transc 33.2 21 0.00045 32.2 1.0 16 44-59 117-132 (267)
126 PF03966 Trm112p: Trm112p-like 33.2 24 0.00053 24.9 1.2 36 45-81 8-61 (68)
127 PF00097 zf-C3HC4: Zinc finger 32.9 25 0.00055 21.7 1.1 18 57-79 24-41 (41)
128 KOG3608 Zn finger proteins [Ge 32.8 41 0.0009 32.5 3.0 38 44-82 263-301 (467)
129 PRK04023 DNA polymerase II lar 32.5 20 0.00043 38.4 0.9 38 43-84 637-674 (1121)
130 PRK10220 hypothetical protein; 32.0 26 0.00056 28.2 1.3 10 73-82 20-29 (111)
131 PF14353 CpXC: CpXC protein 31.8 22 0.00049 27.5 0.9 13 43-55 37-49 (128)
132 PF10276 zf-CHCC: Zinc-finger 30.9 17 0.00037 24.0 0.1 11 44-54 29-39 (40)
133 KOG2817 Predicted E3 ubiquitin 30.9 22 0.00048 34.1 0.8 15 42-56 372-386 (394)
134 COG1675 TFA1 Transcription ini 30.4 38 0.00082 29.0 2.1 31 41-83 110-142 (176)
135 PF09862 DUF2089: Protein of u 30.4 13 0.00027 29.8 -0.7 13 47-59 1-13 (113)
136 COG5109 Uncharacterized conser 30.0 23 0.00051 33.5 0.8 12 42-53 374-385 (396)
137 PF10058 DUF2296: Predicted in 29.8 25 0.00055 24.4 0.8 9 44-52 44-52 (54)
138 KOG2879 Predicted E3 ubiquitin 29.3 14 0.00029 34.2 -0.8 42 42-83 237-286 (298)
139 PF13824 zf-Mss51: Zinc-finger 29.1 26 0.00056 24.9 0.7 13 41-53 11-23 (55)
140 PF14968 CCDC84: Coiled coil p 28.8 28 0.0006 32.6 1.1 26 39-64 53-85 (336)
141 cd03021 DsbA_GSTK DsbA family, 27.7 14 0.00031 30.7 -0.9 14 40-53 4-17 (209)
142 COG4391 Uncharacterized protei 27.6 29 0.00063 25.3 0.8 13 70-82 45-57 (62)
143 PF00301 Rubredoxin: Rubredoxi 27.6 25 0.00055 23.9 0.5 14 39-52 29-42 (47)
144 PRK11088 rrmA 23S rRNA methylt 27.4 17 0.00038 31.4 -0.5 30 44-75 2-34 (272)
145 COG1198 PriA Primosomal protei 27.0 28 0.0006 35.8 0.8 41 40-82 440-484 (730)
146 cd03024 DsbA_FrnE DsbA family, 26.5 19 0.0004 29.0 -0.4 23 41-63 3-26 (201)
147 PF09538 FYDLN_acid: Protein o 26.2 53 0.0012 25.9 2.1 34 40-86 5-39 (108)
148 COG1997 RPL43A Ribosomal prote 26.2 12 0.00026 29.0 -1.5 33 38-82 29-62 (89)
149 PF14828 Amnionless: Amnionles 26.1 38 0.00082 32.5 1.5 42 46-88 193-241 (437)
150 cd02972 DsbA_family DsbA famil 25.6 19 0.00041 24.3 -0.4 11 43-53 5-15 (98)
151 PF04981 NMD3: NMD3 family ; 25.6 41 0.00089 29.1 1.6 11 72-82 34-44 (236)
152 PF10609 ParA: ParA/MinD ATPas 25.4 26 0.00057 26.4 0.3 17 39-55 60-76 (81)
153 KOG3608 Zn finger proteins [Ge 25.2 64 0.0014 31.2 2.8 55 44-98 319-379 (467)
154 cd03022 DsbA_HCCA_Iso DsbA fam 24.9 18 0.00039 28.7 -0.7 13 41-53 3-15 (192)
155 PF14570 zf-RING_4: RING/Ubox 24.6 43 0.00094 23.0 1.2 33 42-81 13-45 (48)
156 cd03019 DsbA_DsbA DsbA family, 24.6 26 0.00056 27.3 0.1 11 43-53 23-33 (178)
157 PRK00564 hypA hydrogenase nick 24.0 31 0.00066 27.1 0.4 31 40-82 67-97 (117)
158 KOG3993 Transcription factor ( 23.9 23 0.0005 34.6 -0.3 34 42-75 456-490 (500)
159 KOG3940 Uncharacterized conser 23.9 44 0.00094 31.5 1.4 24 39-62 15-38 (351)
160 PF11290 DUF3090: Protein of u 23.8 36 0.00079 29.2 0.9 14 45-58 155-168 (171)
161 PF06957 COPI_C: Coatomer (COP 23.6 44 0.00096 32.2 1.5 33 43-88 379-412 (422)
162 smart00586 ZnF_DBF Zinc finger 23.4 39 0.00084 23.4 0.8 22 70-92 2-23 (49)
163 PHA02929 N1R/p28-like protein; 23.3 13 0.00028 33.1 -2.0 43 42-84 172-227 (238)
164 PF14471 DUF4428: Domain of un 23.3 16 0.00034 25.1 -1.2 30 46-83 1-30 (51)
165 COG3058 FdhE Uncharacterized p 23.2 30 0.00064 32.2 0.2 18 72-89 184-201 (308)
166 COG2331 Uncharacterized protei 23.0 26 0.00057 26.8 -0.1 37 43-87 11-47 (82)
167 PF04267 SoxD: Sarcosine oxida 22.8 28 0.00061 26.5 0.0 8 45-52 2-9 (84)
168 PF13462 Thioredoxin_4: Thiore 22.6 16 0.00035 27.9 -1.4 22 42-63 19-41 (162)
169 PF14311 DUF4379: Domain of un 22.5 62 0.0013 21.7 1.7 32 40-79 24-55 (55)
170 PF12013 DUF3505: Protein of u 22.5 52 0.0011 24.9 1.4 31 69-99 7-38 (109)
171 KOG1074 Transcriptional repres 22.3 33 0.00072 36.1 0.4 47 44-92 353-402 (958)
172 PF13719 zinc_ribbon_5: zinc-r 22.3 59 0.0013 20.6 1.4 32 45-82 3-34 (37)
173 PRK14714 DNA polymerase II lar 22.0 40 0.00088 36.9 1.0 36 44-83 667-702 (1337)
174 COG2761 FrnE Predicted dithiol 22.0 27 0.00058 31.0 -0.3 53 40-97 9-69 (225)
175 CHL00174 accD acetyl-CoA carbo 21.9 53 0.0011 30.3 1.6 29 44-82 38-66 (296)
176 PRK05978 hypothetical protein; 21.7 73 0.0016 26.6 2.2 27 44-82 33-61 (148)
177 PF11789 zf-Nse: Zinc-finger o 21.6 65 0.0014 22.4 1.6 21 53-78 33-53 (57)
178 PF12760 Zn_Tnp_IS1595: Transp 21.3 45 0.00098 21.8 0.8 10 43-52 17-26 (46)
179 PHA00733 hypothetical protein 21.1 74 0.0016 25.4 2.1 25 44-68 99-124 (128)
180 cd03023 DsbA_Com1_like DsbA fa 20.9 28 0.0006 26.0 -0.4 11 43-53 13-23 (154)
181 PF13717 zinc_ribbon_4: zinc-r 20.6 64 0.0014 20.4 1.3 31 45-81 3-33 (36)
182 TIGR00515 accD acetyl-CoA carb 20.4 62 0.0014 29.4 1.7 29 44-82 26-54 (285)
183 PRK05654 acetyl-CoA carboxylas 20.3 60 0.0013 29.6 1.6 29 44-82 27-55 (292)
No 1
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=99.80 E-value=2.9e-20 Score=127.49 Aligned_cols=54 Identities=37% Similarity=0.865 Sum_probs=52.2
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccchhhhhhhhhhcc
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHITMQHG 96 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d~v~Hlt~qH~ 96 (200)
++|+||||+++||+.+|+.|+.++|+.+.+++|||||+.+++.||++||+.+||
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 379999999999999999999999999999999999999999999999999996
No 2
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=99.79 E-value=4.1e-20 Score=143.57 Aligned_cols=59 Identities=59% Similarity=0.745 Sum_probs=53.0
Q ss_pred ccccchhhhhccccccccCCC-CcccCCCCCCCCcchhhcccCCCCCCCCCCCCCCCCCC
Q 028989 115 TFSLLRKELRDGNLQSLLGGS-SCFVSSSNTEADPLLSSFIFNTPKVDEPLSVQPLSITE 173 (200)
Q Consensus 115 ~~s~l~k~lre~~lq~llgg~-s~~~s~sn~~pDPLLSsFi~~~~~~~~~~~~~~~~~~e 173 (200)
|+++|+|||||||||+||||+ ++..+++|++|||||||||||+|.++.++.+++....+
T Consensus 1 tlsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~ 60 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSE 60 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCccccccCCcccccc
Confidence 689999999999999999999 55667889999999999999999999988888776655
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=99.02 E-value=2.8e-10 Score=104.64 Aligned_cols=122 Identities=20% Similarity=0.365 Sum_probs=87.4
Q ss_pred ccccchhhcCCCCCCCCCCCccceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccccc---------hhhhhh
Q 028989 21 QSRSDLFIGGGYDETDGDDDLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG---------TDIVSH 90 (200)
Q Consensus 21 qs~~d~~~~~g~ee~e~d~d~r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~---------~d~v~H 90 (200)
..++|+|| |+|-+-- +..+.|+||||++. |.+..+.+|+...|+.....+|||||+.... .+...|
T Consensus 60 ~~dfeL~f--~Ge~i~~--y~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~~qp~~~~~~~~~~~~ 135 (381)
T KOG1280|consen 60 RVDFELYF--GGEPISH--YDPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPEMQPIHSKETENLSVH 135 (381)
T ss_pred ccceeeEe--cCccccc--cccccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcccCchhhhhhhhhhhh
Confidence 45789998 8888743 44449999999996 9999999999999999999999999999732 244444
Q ss_pred hhhhccchhhh---hcccccccCCCCCccccchhhhhccccccc--cCCC-Ccc-c--CCCCC-CCCcc
Q 028989 91 ITMQHGNFFKI---QRKRRLRRGGPNSTFSLLRKELRDGNLQSL--LGGS-SCF-V--SSSNT-EADPL 149 (200)
Q Consensus 91 lt~qH~~~~K~---~r~rk~rr~~~~s~~s~l~k~lre~~lq~l--lgg~-s~~-~--s~sn~-~pDPL 149 (200)
+ .|.+..+- .+.|+..++ .+.+.++.+..+|..++++. +||+ |+. . +++|. ..||+
T Consensus 136 ~--~~~a~~r~~~e~~~r~~~~~-r~~g~~lv~~r~rr~~mh~~~s~~g~~Ss~~ls~spgdr~~~dpi 201 (381)
T KOG1280|consen 136 W--TEIALGRPLQDEIGREMALL-RNMGPDLVEDRRRRTEMHTVPSLPGIRSSQRLSTSPGDRPTVDPI 201 (381)
T ss_pred h--hhhcccccchhhhhhhhhhh-ccccccccchhhhhhhhheecccCCccccccccCCCCCCccccHH
Confidence 4 45554321 245566643 77788888888888888765 4444 332 1 24554 58998
No 4
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=94.77 E-value=0.025 Score=30.97 Aligned_cols=23 Identities=30% Similarity=0.674 Sum_probs=17.1
Q ss_pred ecCCCCccc-ccHHHHHhhhhhcC
Q 028989 45 FLCPFCAED-FDIVGLCCHIDEDH 67 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~~eH 67 (200)
|.||+|+.. -+...|..|+...|
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 689999986 77888888888776
No 5
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=94.57 E-value=0.054 Score=51.27 Aligned_cols=52 Identities=31% Similarity=0.517 Sum_probs=42.0
Q ss_pred eecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccc-------------------------------cc-------
Q 028989 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKR-------------------------------VG------- 84 (200)
Q Consensus 44 ~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~-------------------------------v~------- 84 (200)
-=.|-||... +|..+|..||.+.|- .|-||..+ ++
T Consensus 220 HP~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~~ 293 (493)
T COG5236 220 HPLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFPY 293 (493)
T ss_pred CchhhhccceecChHHHHHHHHhhhh------hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEecc
Confidence 3479999985 999999999999985 57777664 11
Q ss_pred -hhhhhhhhhhccchhhh
Q 028989 85 -TDIVSHITMQHGNFFKI 101 (200)
Q Consensus 85 -~d~v~Hlt~qH~~~~K~ 101 (200)
..+..||+..|+...|.
T Consensus 294 ~~el~~h~~~~h~~~~~~ 311 (493)
T COG5236 294 HTELLEHLTRFHKVNARL 311 (493)
T ss_pred HHHHHHHHHHHhhccccc
Confidence 37889999999999874
No 6
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.08 E-value=0.023 Score=41.68 Aligned_cols=45 Identities=18% Similarity=0.566 Sum_probs=29.2
Q ss_pred CCCCCC-CCCCccceecCCCCccccc--HHHHHhhhhhcCCCCCCcccccccccccc
Q 028989 31 GYDETD-GDDDLNAMFLCPFCAEDFD--IVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 31 g~ee~e-~d~d~r~~F~CPfC~e~fD--~~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
.++|++ ..+....+|||| ||..|. ...|. ..-..+.||-|+..|.
T Consensus 8 eiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 8 EIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLIIR 55 (67)
T ss_pred EeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEEE
Confidence 456666 344566799999 998543 33442 1233478999998754
No 7
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=93.96 E-value=0.015 Score=42.22 Aligned_cols=37 Identities=27% Similarity=0.626 Sum_probs=24.9
Q ss_pred CCccceecCCCCcccccH--HHHHhhhhhcCCCCCCcccccccccccc
Q 028989 39 DDLNAMFLCPFCAEDFDI--VGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~fD~--~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
++..-+|||| ||.-|.+ ..|. ..-+.++||-|+.+|-
T Consensus 17 e~~~ftyPCP-CGDRFeIsLeDl~--------~GE~VArCPSCSLiv~ 55 (67)
T COG5216 17 EEKTFTYPCP-CGDRFEISLEDLR--------NGEVVARCPSCSLIVC 55 (67)
T ss_pred CCceEEecCC-CCCEeEEEHHHhh--------CCceEEEcCCceEEEE
Confidence 3566799999 9885554 3332 2234578999998854
No 8
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=93.05 E-value=0.064 Score=48.74 Aligned_cols=37 Identities=24% Similarity=0.572 Sum_probs=25.4
Q ss_pred cceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 42 NAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 42 r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
+..|.||+|++. +.+..|--||...= -.-+|+||...
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 667888888884 88888888887652 23355565554
No 9
>PHA00732 hypothetical protein
Probab=92.74 E-value=0.12 Score=38.50 Aligned_cols=42 Identities=31% Similarity=0.723 Sum_probs=33.7
Q ss_pred ecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccccchhhhhhh
Q 028989 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHI 91 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d~v~Hl 91 (200)
|.|+.|++. -....|..|+...|.. ..|++|..... ++..|+
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 789999997 5888999999865642 26999998866 677776
No 10
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=92.30 E-value=0.077 Score=29.64 Aligned_cols=21 Identities=24% Similarity=0.626 Sum_probs=15.6
Q ss_pred ecCCCCccc-ccHHHHHhhhhh
Q 028989 45 FLCPFCAED-FDIVGLCCHIDE 65 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~~ 65 (200)
|.||.|++. -+...|..|+..
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 678888886 567777777765
No 11
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=92.02 E-value=0.081 Score=37.81 Aligned_cols=48 Identities=25% Similarity=0.545 Sum_probs=14.4
Q ss_pred cCCCCccc-ccHHHHHhhhhhcCCCCCC---------------------cccccccccccc--hhhhhhhhh
Q 028989 46 LCPFCAED-FDIVGLCCHIDEDHPIEAK---------------------NGVCPVCAKRVG--TDIVSHITM 93 (200)
Q Consensus 46 ~CPfC~e~-fD~~~Lc~H~~~eH~~e~k---------------------~vVCPICa~~v~--~d~v~Hlt~ 93 (200)
.|+||+.. -+...|..|+...|.+... .-.|++|..... ..+..||+.
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 39999997 6688899999999987432 123999999853 589999963
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=91.63 E-value=0.17 Score=49.86 Aligned_cols=45 Identities=22% Similarity=0.440 Sum_probs=36.0
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCccccccccccc-chhhhhhhh
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV-GTDIVSHIT 92 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v-~~d~v~Hlt 92 (200)
.-+.||+|++.|....|-.|....| +.+.|| |...+ ..+|..|++
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~ 497 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQA 497 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhh
Confidence 3468999999988899999999876 678999 97543 358888875
No 13
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.46 E-value=0.15 Score=30.20 Aligned_cols=21 Identities=29% Similarity=0.608 Sum_probs=18.6
Q ss_pred eecCCCCcccccHHHHHhhhh
Q 028989 44 MFLCPFCAEDFDIVGLCCHID 64 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~ 64 (200)
..+||+|+..|....|-.|+.
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 468999999999999999974
No 14
>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=90.87 E-value=0.16 Score=35.91 Aligned_cols=26 Identities=19% Similarity=0.666 Sum_probs=17.2
Q ss_pred Ccccccccccccc--hhhhhhhhhhccc
Q 028989 72 KNGVCPVCAKRVG--TDIVSHITMQHGN 97 (200)
Q Consensus 72 k~vVCPICa~~v~--~d~v~Hlt~qH~~ 97 (200)
.+..||+|.+.+. .|+-.|+.+.|+.
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 3479999999855 6999999887763
No 15
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=90.20 E-value=0.19 Score=28.54 Aligned_cols=24 Identities=29% Similarity=0.704 Sum_probs=17.6
Q ss_pred ecCCCCcccccHHHHHhhhhhcCC
Q 028989 45 FLCPFCAEDFDIVGLCCHIDEDHP 68 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~eH~ 68 (200)
|.||+|...-....|..|+...|+
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 689999886448889999988775
No 16
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.92 E-value=0.28 Score=39.65 Aligned_cols=41 Identities=22% Similarity=0.547 Sum_probs=27.8
Q ss_pred CCccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccc
Q 028989 39 DDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
+.....|.||.|+..|+...-....+ + ....+||.|...+-
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEELE 134 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEEE
Confidence 34567999999999766544333222 2 34489999998854
No 17
>PHA00733 hypothetical protein
Probab=87.50 E-value=0.72 Score=36.90 Aligned_cols=50 Identities=30% Similarity=0.652 Sum_probs=36.1
Q ss_pred ceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccccc--hhhhhhhhhhcc
Q 028989 43 AMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG--TDIVSHITMQHG 96 (200)
Q Consensus 43 ~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~--~d~v~Hlt~qH~ 96 (200)
..|.|+.|++. -....|..|+.. | .....|++|..... .++..|+.--|+
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 35899999997 556778888874 2 23469999988743 588888866555
No 18
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=87.25 E-value=0.48 Score=43.20 Aligned_cols=47 Identities=26% Similarity=0.471 Sum_probs=26.9
Q ss_pred eecCCCCcccccHHH-HHhhhhhcCCCCCCcccccccccccch--hhhhhhh
Q 028989 44 MFLCPFCAEDFDIVG-LCCHIDEDHPIEAKNGVCPVCAKRVGT--DIVSHIT 92 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~-Lc~H~~~eH~~e~k~vVCPICa~~v~~--d~v~Hlt 92 (200)
-+.|++||+-|+..= |.-||+.. ..-|+-.||.|..-..+ |+-+||+
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTH--TGEKPF~C~hC~kAFADRSNLRAHmQ 236 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTH--TGEKPFSCPHCGKAFADRSNLRAHMQ 236 (279)
T ss_pred CcccccccccccchHHhhcccccc--cCCCCccCCcccchhcchHHHHHHHH
Confidence 366666666666443 34455544 33455666666666543 6666664
No 19
>PHA02768 hypothetical protein; Provisional
Probab=86.94 E-value=0.57 Score=33.17 Aligned_cols=34 Identities=21% Similarity=0.484 Sum_probs=25.7
Q ss_pred eecCCCCccc-ccHHHHHhhhhhcCCCCCCccccccccc
Q 028989 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (200)
Q Consensus 44 ~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~ 81 (200)
-|.||.|++. -....|..|...++ ++.-|..|..
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 4789999996 67788999998854 4556777765
No 20
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=86.68 E-value=0.27 Score=30.95 Aligned_cols=33 Identities=21% Similarity=0.573 Sum_probs=23.0
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
.+|.||-|+..|++..-. .+....+||.|.+.+
T Consensus 4 Y~y~C~~Cg~~fe~~~~~--------~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKI--------SDDPLATCPECGGDV 36 (41)
T ss_pred EEEEcCCCCCEEEEEEec--------CCCCCCCCCCCCCcc
Confidence 479999999987643221 114567899999853
No 21
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=84.81 E-value=0.57 Score=45.48 Aligned_cols=36 Identities=31% Similarity=0.625 Sum_probs=31.4
Q ss_pred CCCccceecCCCCcccc-cHHHHHhhhhhcCCCCCCc
Q 028989 38 DDDLNAMFLCPFCAEDF-DIVGLCCHIDEDHPIEAKN 73 (200)
Q Consensus 38 d~d~r~~F~CPfC~e~f-D~~~Lc~H~~~eH~~e~k~ 73 (200)
.++.++-|.||+|.++| .+..|-+|++.+|+.|-+.
T Consensus 9 s~~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ed~~ 45 (505)
T KOG1842|consen 9 SGEILEGFLCPICLLDLPNLSALNDHLDVEHFEEDEK 45 (505)
T ss_pred cchhhhcccCchHhhhhhhHHHHHHHHhhhccccchh
Confidence 46788999999999985 5789999999999998864
No 22
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=84.80 E-value=0.31 Score=34.23 Aligned_cols=30 Identities=20% Similarity=0.557 Sum_probs=21.9
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
.|.||-|++.+++..... .-.+.||.|.+.
T Consensus 2 ~~~CP~CG~~iev~~~~~---------GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL---------GELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCcc---------CCEEeCCCCCCE
Confidence 589999999876654321 225799999986
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=84.59 E-value=0.94 Score=44.85 Aligned_cols=39 Identities=18% Similarity=0.332 Sum_probs=28.4
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccc
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
..+.|| |+..+.-..|-.|+.. |+-. +...|+.|...+.
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~t-hCp~-Kpi~C~fC~~~v~ 515 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQAS-TCPL-RLITCRFCGDMVQ 515 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhhc-cCCC-CceeCCCCCCccc
Confidence 457888 8877778888888754 4443 6678888887763
No 24
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=84.56 E-value=0.61 Score=29.31 Aligned_cols=33 Identities=21% Similarity=0.439 Sum_probs=20.6
Q ss_pred ecCCCCcccccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
+.||.|+..|.+..-. ...+...+.||.|...+
T Consensus 3 ~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHH------cCCCCCEEECCCCCCEE
Confidence 6899999865544321 12233468899997653
No 25
>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=83.41 E-value=1.2 Score=29.88 Aligned_cols=29 Identities=10% Similarity=0.209 Sum_probs=21.4
Q ss_pred CcccccHHHHHhhhhhcCCCCCCcccccccccccch
Q 028989 50 CAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (200)
Q Consensus 50 C~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~ 85 (200)
||.-|+...+..++.. ...||+|...++.
T Consensus 19 ~G~v~~~~~i~~~~~~-------~~~cP~~~~~~~~ 47 (63)
T smart00504 19 SGQTYERRAIEKWLLS-------HGTDPVTGQPLTH 47 (63)
T ss_pred CCCEEeHHHHHHHHHH-------CCCCCCCcCCCCh
Confidence 3445888888888865 3689999987753
No 26
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=83.40 E-value=0.42 Score=34.91 Aligned_cols=31 Identities=26% Similarity=0.531 Sum_probs=20.7
Q ss_pred ecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccccc
Q 028989 45 FLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
=|||||+.+ +++. |..-.-.++|.-|.+...
T Consensus 7 KPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 7 KPCPFCGCPSVTVK---------AISGYYRAKCNGCESRTG 38 (64)
T ss_pred cCCCCCCCceeEEE---------ecCceEEEEcCCCCcCcc
Confidence 389999986 4443 222233589999999633
No 27
>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=83.03 E-value=0.41 Score=31.21 Aligned_cols=35 Identities=29% Similarity=0.613 Sum_probs=22.1
Q ss_pred ecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccchhhhh
Q 028989 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVS 89 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d~v~ 89 (200)
|.||.|+... + +.+ .+....||+.|...+..+.+.
T Consensus 1 m~Cp~Cg~~~-~------~~D---~~~g~~vC~~CG~Vl~e~~i~ 35 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VFD---PERGELVCPNCGLVLEENIID 35 (43)
T ss_dssp ESBTTTSSSE-E------EEE---TTTTEEEETTT-BBEE-TTBS
T ss_pred CCCcCCcCCc-e------EEc---CCCCeEECCCCCCEeeccccc
Confidence 6899999853 1 111 345567999998887766653
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=81.20 E-value=1.2 Score=31.67 Aligned_cols=26 Identities=31% Similarity=0.719 Sum_probs=21.3
Q ss_pred ceecCCCCcccc-cHHHHHhhhhhcCC
Q 028989 43 AMFLCPFCAEDF-DIVGLCCHIDEDHP 68 (200)
Q Consensus 43 ~~F~CPfC~e~f-D~~~Lc~H~~~eH~ 68 (200)
..|.|++|++.| +...|..|+...|-
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 369999999985 89999999998743
No 29
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=81.19 E-value=0.8 Score=30.83 Aligned_cols=45 Identities=31% Similarity=0.610 Sum_probs=30.0
Q ss_pred eecCCC--CcccccHHHHHhhhhhcCCCCCCcccccc----cccccch-hhhhh
Q 028989 44 MFLCPF--CAEDFDIVGLCCHIDEDHPIEAKNGVCPV----CAKRVGT-DIVSH 90 (200)
Q Consensus 44 ~F~CPf--C~e~fD~~~Lc~H~~~eH~~e~k~vVCPI----Ca~~v~~-d~v~H 90 (200)
...||+ |.+.+-...|-.|+..+=+ -+.+.||- |..++.. +|..|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~--~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECP--KRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTST--TSEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCC--CCcEECCCCCCCCCCccchhHHhCC
Confidence 468999 7777888999999997633 45789999 9998664 56554
No 30
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=80.34 E-value=1.1 Score=29.80 Aligned_cols=32 Identities=19% Similarity=0.664 Sum_probs=22.5
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
.+|.|+-|+..|++. ....+ ...+.||.|...
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 479999999988853 12222 345789999983
No 31
>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=79.80 E-value=0.93 Score=28.25 Aligned_cols=25 Identities=36% Similarity=0.873 Sum_probs=17.0
Q ss_pred ecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
|.|+-||..+|... .+-+||+|.+.
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCCc
Confidence 67888887555433 45689999764
No 32
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=78.34 E-value=0.63 Score=40.05 Aligned_cols=49 Identities=18% Similarity=0.430 Sum_probs=27.9
Q ss_pred eecCCCCcccccHHHHHh--------------hhhhcCCCCCCcccccccccccchhhhhhhh
Q 028989 44 MFLCPFCAEDFDIVGLCC--------------HIDEDHPIEAKNGVCPVCAKRVGTDIVSHIT 92 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~--------------H~~~eH~~e~k~vVCPICa~~v~~d~v~Hlt 92 (200)
++.||+|+.+|....+.. |=...-|.==...|||-|----..+...+|+
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~ 67 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLS 67 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCC
Confidence 579999999887654332 2222222222346899998764433223454
No 33
>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=78.09 E-value=1.7 Score=24.93 Aligned_cols=24 Identities=21% Similarity=0.368 Sum_probs=18.3
Q ss_pred ecCCCCccc-ccHHHHHhhhhhcCC
Q 028989 45 FLCPFCAED-FDIVGLCCHIDEDHP 68 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~~eH~ 68 (200)
|.|..|++. -+...|..|....|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhcC
Confidence 788888886 678888888866543
No 34
>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=77.84 E-value=0.79 Score=28.72 Aligned_cols=24 Identities=29% Similarity=0.913 Sum_probs=12.6
Q ss_pred cCCCCcccccHHHHHhhhhhcCCCCCCccccccccc
Q 028989 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~ 81 (200)
+||.|+.++.. .|....|||-|..
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 69999886544 4566789999974
No 35
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=76.80 E-value=1.1 Score=38.80 Aligned_cols=49 Identities=27% Similarity=0.588 Sum_probs=30.1
Q ss_pred CccceecCCCCccccc--HHHHHhhh-----hhcCC--------------CCCCcccccccccccchhhh
Q 028989 40 DLNAMFLCPFCAEDFD--IVGLCCHI-----DEDHP--------------IEAKNGVCPVCAKRVGTDIV 88 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD--~~~Lc~H~-----~~eH~--------------~e~k~vVCPICa~~v~~d~v 88 (200)
+....|.||.|.+.+. +...|-|+ -.+.. ...+...||+|...++.+-+
T Consensus 14 ~~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L 83 (193)
T PLN03208 14 DSGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL 83 (193)
T ss_pred cCCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence 3456899999998633 33446662 32211 02234689999999886444
No 36
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=76.56 E-value=2.1 Score=30.79 Aligned_cols=34 Identities=29% Similarity=0.693 Sum_probs=25.5
Q ss_pred CccceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccc
Q 028989 40 DLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCA 80 (200)
Q Consensus 40 d~r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa 80 (200)
|....|.||-|++. +-. |..|... ++..+||-|-
T Consensus 21 ~~~~~F~CPnCG~~~I~R---C~~CRk~----~~~Y~CP~CG 55 (59)
T PRK14890 21 EKAVKFLCPNCGEVIIYR---CEKCRKQ----SNPYTCPKCG 55 (59)
T ss_pred CccCEeeCCCCCCeeEee---chhHHhc----CCceECCCCC
Confidence 44679999999996 433 6666665 6778999995
No 37
>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=76.09 E-value=2.1 Score=25.60 Aligned_cols=19 Identities=26% Similarity=0.607 Sum_probs=10.1
Q ss_pred cCCCCcccccHHHHHhhhh
Q 028989 46 LCPFCAEDFDIVGLCCHID 64 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~~ 64 (200)
.||-|++.+....+-.|++
T Consensus 3 ~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREVPENLINSHLD 21 (26)
T ss_pred cCCCCcCcccHHHHHHHHH
Confidence 4555555555555555554
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=75.83 E-value=1.2 Score=45.75 Aligned_cols=51 Identities=24% Similarity=0.531 Sum_probs=41.0
Q ss_pred cceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccccc--hhhhhhhh
Q 028989 42 NAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG--TDIVSHIT 92 (200)
Q Consensus 42 r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~--~d~v~Hlt 92 (200)
.+..+||||+.. -.+..|.+||.-.|---.-|.-|+.|+.... ..+-+|++
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytFAyRtQLErhm~ 261 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTFAYRTQLERHMQ 261 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhhhhHHHHHHHHH
Confidence 356899999995 7789999999999998888889999999743 35555554
No 39
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=75.41 E-value=0.93 Score=35.36 Aligned_cols=37 Identities=19% Similarity=0.424 Sum_probs=22.9
Q ss_pred ccceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccccchh
Q 028989 41 LNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTD 86 (200)
Q Consensus 41 ~r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d 86 (200)
....|.||+|++. +.+ .-.+ ..-.++||+|-...+..
T Consensus 18 lpt~f~CP~Cge~~v~v-------~~~k--~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 18 LPKIFECPRCGKVSISV-------KIKK--NIAIITCGNCGLYTEFE 55 (99)
T ss_pred CCcEeECCCCCCeEeee-------ecCC--CcceEECCCCCCccCEE
Confidence 3468999999952 211 1111 13347999999986653
No 40
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=74.93 E-value=1.6 Score=27.58 Aligned_cols=26 Identities=23% Similarity=0.721 Sum_probs=17.7
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
.|.|+-||..++... .+.+||||.+.
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 478999987654321 23599999874
No 41
>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=74.72 E-value=2.6 Score=35.17 Aligned_cols=54 Identities=22% Similarity=0.391 Sum_probs=33.5
Q ss_pred ceecCCC----CcccccHHHHHhhhhhcCCCCCCcccccc----cccc-cchhhhhhhhhhccchh
Q 028989 43 AMFLCPF----CAEDFDIVGLCCHIDEDHPIEAKNGVCPV----CAKR-VGTDIVSHITMQHGNFF 99 (200)
Q Consensus 43 ~~F~CPf----C~e~fD~~~Lc~H~~~eH~~e~k~vVCPI----Ca~~-v~~d~v~Hlt~qH~~~~ 99 (200)
-.|||+| |.+.+-......|.++= .-++.-||+ |.-. ...++..|++..|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~~C---~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEEEC---PFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHHT----TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhccC---CCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 4799999 99988888898897543 345678999 7543 44699999999999854
No 42
>PHA00616 hypothetical protein
Probab=74.67 E-value=2 Score=29.16 Aligned_cols=25 Identities=16% Similarity=0.174 Sum_probs=17.3
Q ss_pred ecCCCCccc-ccHHHHHhhhhhcCCC
Q 028989 45 FLCPFCAED-FDIVGLCCHIDEDHPI 69 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~~eH~~ 69 (200)
|.||.||.. .....|-.|+...|--
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 567777775 6667777777766654
No 43
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=73.23 E-value=3.1 Score=34.33 Aligned_cols=36 Identities=25% Similarity=0.491 Sum_probs=26.3
Q ss_pred CCccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccc
Q 028989 39 DDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
+.....|.||-|+..|....-.. .+-.||+|...+-
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAMLD 139 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEee
Confidence 44577999999998655555543 2579999999743
No 44
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=72.90 E-value=3.1 Score=35.12 Aligned_cols=36 Identities=25% Similarity=0.558 Sum_probs=25.1
Q ss_pred CCccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccc
Q 028989 39 DDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
+...+.|.||-|+..|....-.. ..-.||+|...+-
T Consensus 112 e~~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEMLE 147 (178)
T ss_pred ccCCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCCe
Confidence 34568999999998654444321 2569999999843
No 45
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=72.86 E-value=2.5 Score=27.82 Aligned_cols=29 Identities=21% Similarity=0.667 Sum_probs=18.1
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
+|.||-|+..++.... .....||-|..++
T Consensus 3 ~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY-----------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC-----------CCceECCCCCCeE
Confidence 5788888876655211 1156788887653
No 46
>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=71.31 E-value=3.2 Score=40.36 Aligned_cols=41 Identities=24% Similarity=0.529 Sum_probs=32.4
Q ss_pred cceecCCCCccc-ccHHHHHhhhhhcCCCCCCc---ccccccccc
Q 028989 42 NAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKN---GVCPVCAKR 82 (200)
Q Consensus 42 r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~---vVCPICa~~ 82 (200)
|.--.||+|.+. .|...+..|+..+|+..-.+ -+.|-+...
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~ 99 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDD 99 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCH
Confidence 456789999985 99999999999999997755 355655444
No 47
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=71.18 E-value=1.8 Score=29.55 Aligned_cols=31 Identities=26% Similarity=0.526 Sum_probs=18.4
Q ss_pred eecCCCCccc-ccHHHHHhhhhhcCCCCC---Cccccccccc
Q 028989 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEA---KNGVCPVCAK 81 (200)
Q Consensus 44 ~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~---k~vVCPICa~ 81 (200)
.-+|||||.. +.+.. ....+. -.+.|..|.+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 4589999974 32222 222222 3467999987
No 48
>smart00355 ZnF_C2H2 zinc finger.
Probab=70.24 E-value=4.4 Score=21.69 Aligned_cols=20 Identities=25% Similarity=0.491 Sum_probs=13.7
Q ss_pred ecCCCCccc-ccHHHHHhhhh
Q 028989 45 FLCPFCAED-FDIVGLCCHID 64 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~ 64 (200)
|.|+.|++. -....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 467777775 55667777766
No 49
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=68.82 E-value=1.7 Score=30.27 Aligned_cols=32 Identities=28% Similarity=0.776 Sum_probs=18.1
Q ss_pred ecCCCCcccccHHHHHhhhhhcCCCCCCcc--ccccccccc
Q 028989 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNG--VCPVCAKRV 83 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~v--VCPICa~~v 83 (200)
+.||||++.+++. .......... =|+||-..+
T Consensus 1 i~CPyCge~~~~~-------iD~s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEIL-------IDPSAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEEE-------EecCCCCeeEEeehhhcCCcc
Confidence 3699999976542 1111222222 399988763
No 50
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=66.86 E-value=1.3 Score=28.95 Aligned_cols=31 Identities=26% Similarity=0.688 Sum_probs=22.4
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCccccccccc
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~ 81 (200)
.+|.|+=|+..|++..- +. +...++||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~---~~-----~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQS---IS-----EDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEE---cC-----CCCCCcCCCCCC
Confidence 47999999988775432 21 245689999988
No 51
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=66.55 E-value=2.7 Score=31.60 Aligned_cols=27 Identities=33% Similarity=0.827 Sum_probs=17.8
Q ss_pred eecCCCCccc-ccHHHHHhhhhhcCCCCCCccccccccc
Q 028989 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (200)
Q Consensus 44 ~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~ 81 (200)
.|+||-|+.. |+..+ +..--+||||-=
T Consensus 1 K~~CPCCg~~Tl~~~~-----------~~~ydIC~VC~W 28 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERG-----------EGTYDICPVCFW 28 (78)
T ss_pred CccCCCCCcEEeccCC-----------CcCceECCCCCc
Confidence 3799999974 54322 222459999964
No 52
>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=66.39 E-value=8.7 Score=27.43 Aligned_cols=38 Identities=18% Similarity=0.477 Sum_probs=23.8
Q ss_pred cceecCCCCcc------------cccHHHHHhhhhhcCCCCCCcccccccccccch
Q 028989 42 NAMFLCPFCAE------------DFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (200)
Q Consensus 42 r~~F~CPfC~e------------~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~ 85 (200)
+.+|.||.|++ -||...+..++.. ...+||+|...++.
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLSE 51 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-SG
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCCc
Confidence 35677877765 3666777777766 56799999887665
No 53
>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=66.03 E-value=2.4 Score=31.69 Aligned_cols=35 Identities=29% Similarity=0.593 Sum_probs=14.2
Q ss_pred cceecCCCCc-cc-ccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 42 NAMFLCPFCA-ED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 42 r~~F~CPfC~-e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
...|.||||+ +. +.+. -......-.+.|-+|....
T Consensus 20 ~~~F~CPfC~~~~sV~v~-------idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVK-------IDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp SS----TTT--SS-EEEE-------EETTTTEEEEEESSS--EE
T ss_pred CceEcCCcCCCCCeEEEE-------EEccCCEEEEEecCCCCeE
Confidence 4589999999 43 3221 1111223346799997763
No 54
>PF12773 DZR: Double zinc ribbon
Probab=65.43 E-value=3.7 Score=26.96 Aligned_cols=28 Identities=25% Similarity=0.822 Sum_probs=19.5
Q ss_pred cCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccch
Q 028989 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~ 85 (200)
.||.|+..+. ..+....+||.|.+.+..
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAENPP 41 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCCCcC
Confidence 6888887766 344556789999887543
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=64.14 E-value=5.2 Score=27.03 Aligned_cols=24 Identities=25% Similarity=0.652 Sum_probs=20.3
Q ss_pred eecCCCCcccccHHHHHhhhhhcCC
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHP 68 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~ 68 (200)
.+.||.|...+.. .|..|+...|.
T Consensus 31 ~v~CPiC~~~~~~-~l~~Hl~~~H~ 54 (54)
T PF05605_consen 31 NVVCPICSSRVTD-NLIRHLNSQHR 54 (54)
T ss_pred CccCCCchhhhhh-HHHHHHHHhcC
Confidence 6899999987664 89999998884
No 56
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=64.12 E-value=1.8 Score=33.49 Aligned_cols=16 Identities=31% Similarity=0.974 Sum_probs=13.1
Q ss_pred CCCccceecCCCCccc
Q 028989 38 DDDLNAMFLCPFCAED 53 (200)
Q Consensus 38 d~d~r~~F~CPfC~e~ 53 (200)
+..+.+.|.||||+..
T Consensus 30 e~~q~a~y~CpfCgk~ 45 (90)
T PTZ00255 30 EISQHAKYFCPFCGKH 45 (90)
T ss_pred HHHHhCCccCCCCCCC
Confidence 4567889999999874
No 57
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=63.88 E-value=1.5 Score=36.86 Aligned_cols=56 Identities=18% Similarity=0.549 Sum_probs=27.4
Q ss_pred cceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccc-hhhhhhhhhhccchh
Q 028989 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG-TDIVSHITMQHGNFF 99 (200)
Q Consensus 42 r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~-~d~v~Hlt~qH~~~~ 99 (200)
+-.|.||.|+..+...++.. .+.-.....-..||-|..... .-++..++++-+...
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~~~~~l~Nql~l~iR~~i 72 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPLSPASLVNQLELQIREHI 72 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B--HHHHHHHHHHHHHHHH
T ss_pred ceEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcCCHHHHHHHHHHHHHHHH
Confidence 44899999999887777644 111112344568999999755 345555555444443
No 58
>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=63.38 E-value=3.1 Score=28.27 Aligned_cols=8 Identities=50% Similarity=1.443 Sum_probs=6.9
Q ss_pred cCCCCccc
Q 028989 46 LCPFCAED 53 (200)
Q Consensus 46 ~CPfC~e~ 53 (200)
+||||+-.
T Consensus 3 PCPfCGg~ 10 (53)
T TIGR03655 3 PCPFCGGA 10 (53)
T ss_pred CCCCCCCc
Confidence 89999973
No 59
>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=61.53 E-value=6.8 Score=27.23 Aligned_cols=42 Identities=17% Similarity=0.342 Sum_probs=30.9
Q ss_pred CccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccchhhhhhhh
Q 028989 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHIT 92 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d~v~Hlt 92 (200)
+.-..=.||.|+..... ....+..+||.|......|..+=++
T Consensus 24 ~~~TSq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~rD~naA~N 65 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMDRDVNAARN 65 (69)
T ss_pred CCCCccCccCccccccc-----------ccccceEEcCCCCCEECcHHHHHHH
Confidence 33366789999875332 4556678999999999988887664
No 60
>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=60.94 E-value=0.68 Score=34.30 Aligned_cols=53 Identities=21% Similarity=0.429 Sum_probs=24.3
Q ss_pred cCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccc-------hhhhhhhhhhccchhhhh
Q 028989 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG-------TDIVSHITMQHGNFFKIQ 102 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~-------~d~v~Hlt~qH~~~~K~~ 102 (200)
.||-|..+++..+---||..=+..=.+.+.||-|...+- .|+. =||+|.+|++
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYF----C~~c~gLiSK 62 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYF----CNHCHGLISK 62 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-T
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhccccee----eccCCceeec
Confidence 566666665555532222222222234578999998742 3554 3588888754
No 61
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.11 E-value=6.1 Score=34.28 Aligned_cols=43 Identities=21% Similarity=0.600 Sum_probs=27.5
Q ss_pred ceecCCCCcccccHHH---------HHhhhhhcCCCCCCcccccccccccchhh
Q 028989 43 AMFLCPFCAEDFDIVG---------LCCHIDEDHPIEAKNGVCPVCAKRVGTDI 87 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~---------Lc~H~~~eH~~e~k~vVCPICa~~v~~d~ 87 (200)
..|.||.|-..+..-. .|.-|..+ .=.+.++||+|..+|+.-.
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~--alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKD--ALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHH--HHHhCCCCCCcccccchhh
Confidence 5799999987655433 33444443 1124468999999887543
No 62
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=58.67 E-value=6.4 Score=22.91 Aligned_cols=21 Identities=24% Similarity=0.396 Sum_probs=14.6
Q ss_pred ecCCCCccc-ccHHHHHhhhhh
Q 028989 45 FLCPFCAED-FDIVGLCCHIDE 65 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~~ 65 (200)
|.|+.|+.. -+...|..|+..
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 677888775 667777777653
No 63
>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=57.80 E-value=4.2 Score=31.53 Aligned_cols=16 Identities=31% Similarity=0.972 Sum_probs=12.9
Q ss_pred CCCccceecCCCCccc
Q 028989 38 DDDLNAMFLCPFCAED 53 (200)
Q Consensus 38 d~d~r~~F~CPfC~e~ 53 (200)
+..+.+.|+||||+..
T Consensus 29 e~~q~a~y~CpfCgk~ 44 (91)
T TIGR00280 29 EIQQKAKYVCPFCGKK 44 (91)
T ss_pred HHHHhcCccCCCCCCC
Confidence 3567889999999864
No 64
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=57.36 E-value=4.4 Score=31.34 Aligned_cols=16 Identities=25% Similarity=0.887 Sum_probs=12.8
Q ss_pred CCCccceecCCCCccc
Q 028989 38 DDDLNAMFLCPFCAED 53 (200)
Q Consensus 38 d~d~r~~F~CPfC~e~ 53 (200)
+..+.+.|+||||+..
T Consensus 30 e~~q~a~y~CpfCgk~ 45 (90)
T PRK03976 30 EEKMRAKHVCPVCGRP 45 (90)
T ss_pred HHHHhcCccCCCCCCC
Confidence 3467889999999764
No 65
>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=56.62 E-value=7.3 Score=26.43 Aligned_cols=23 Identities=26% Similarity=0.501 Sum_probs=12.4
Q ss_pred ccccccccchhhhhhhhhhccch
Q 028989 76 CPVCAKRVGTDIVSHITMQHGNF 98 (200)
Q Consensus 76 CPICa~~v~~d~v~Hlt~qH~~~ 98 (200)
||-|..+.+.|..-+=-+||...
T Consensus 1 CP~C~~kkk~~Y~~~~LlqHA~g 23 (43)
T PF03470_consen 1 CPFCPGKKKQDYKYRELLQHASG 23 (43)
T ss_pred CCCCCCCCCcceehhHHHHHHHh
Confidence 77777776544433333445443
No 66
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.96 E-value=11 Score=27.33 Aligned_cols=35 Identities=23% Similarity=0.450 Sum_probs=22.2
Q ss_pred CCccceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccc
Q 028989 39 DDLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCA 80 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa 80 (200)
+|....|+||-|++. +-.-.- |... .+..+||-|-
T Consensus 22 ~e~~v~F~CPnCGe~~I~Rc~~---CRk~----g~~Y~Cp~CG 57 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYRCAK---CRKL----GNPYRCPKCG 57 (61)
T ss_pred CCceeEeeCCCCCceeeehhhh---HHHc----CCceECCCcC
Confidence 466679999999974 433222 2222 4567899885
No 67
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=54.81 E-value=7.3 Score=33.04 Aligned_cols=48 Identities=17% Similarity=0.301 Sum_probs=34.0
Q ss_pred CCCCCCCCCCccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccchhhhhhhhhh
Q 028989 31 GYDETDGDDDLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIVSHITMQ 94 (200)
Q Consensus 31 g~ee~e~d~d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d~v~Hlt~q 94 (200)
|+..+..+++..+.=.||-||. ...+...||.|......|..+=+++.
T Consensus 296 ~~~~v~~~~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~Ni~ 343 (364)
T COG0675 296 GGIVVKVVPPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALNIA 343 (364)
T ss_pred CCeEEEECCCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHHHHH
Confidence 3333333444555678999998 33567899999999999998888543
No 68
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=54.77 E-value=8.1 Score=27.76 Aligned_cols=48 Identities=21% Similarity=0.418 Sum_probs=23.7
Q ss_pred CCccceecCC--CCcccccHHHHHhhhhhcCC----CCCCcccccccccccchh
Q 028989 39 DDLNAMFLCP--FCAEDFDIVGLCCHIDEDHP----IEAKNGVCPVCAKRVGTD 86 (200)
Q Consensus 39 ~d~r~~F~CP--fC~e~fD~~~Lc~H~~~eH~----~e~k~vVCPICa~~v~~d 86 (200)
++..+...|| -|+.-|-..-|...+..... +....|.||.|...++-.
T Consensus 15 ~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 15 DGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp T-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 3344578887 99999999999999876543 344557799999987644
No 69
>PRK12496 hypothetical protein; Provisional
Probab=54.59 E-value=7.7 Score=32.25 Aligned_cols=28 Identities=21% Similarity=0.532 Sum_probs=20.1
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
.|.|+-|+..|+.. ....+||||...+.
T Consensus 127 ~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPED-------------YPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCC-------------CCCCcCCCCCChhh
Confidence 58999999888631 12248999987653
No 70
>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=53.79 E-value=7.6 Score=23.28 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=10.4
Q ss_pred CccceecCCCCcc
Q 028989 40 DLNAMFLCPFCAE 52 (200)
Q Consensus 40 d~r~~F~CPfC~e 52 (200)
+.-..|+||-|++
T Consensus 12 ~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 12 EQAVPFPCPNCGF 24 (24)
T ss_pred ccCceEeCCCCCC
Confidence 4456899999985
No 71
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=52.96 E-value=9 Score=25.61 Aligned_cols=28 Identities=21% Similarity=0.627 Sum_probs=20.6
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
.|.|.-|+.++++. ....+.||-|..+|
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58899999987754 23457899997653
No 72
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=51.97 E-value=6.5 Score=37.60 Aligned_cols=21 Identities=29% Similarity=0.727 Sum_probs=14.7
Q ss_pred HHhhhhhcCCCCCCcccccccccccc
Q 028989 59 LCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 59 Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
++.||.+. -||-||.|..+..
T Consensus 44 c~~~irq~-----lngrcpacrr~y~ 64 (480)
T COG5175 44 CYNNIRQN-----LNGRCPACRRKYD 64 (480)
T ss_pred HHHHHHhh-----ccCCChHhhhhcc
Confidence 44555544 6899999998744
No 73
>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=51.82 E-value=8.4 Score=26.04 Aligned_cols=19 Identities=21% Similarity=0.908 Sum_probs=8.7
Q ss_pred ccccccccccch----hhhhhhh
Q 028989 74 GVCPVCAKRVGT----DIVSHIT 92 (200)
Q Consensus 74 vVCPICa~~v~~----d~v~Hlt 92 (200)
++||||...++. +++.+++
T Consensus 21 ~~CPlC~r~l~~e~~~~li~~~~ 43 (54)
T PF04423_consen 21 GCCPLCGRPLDEEHRQELIKKYK 43 (54)
T ss_dssp EE-TTT--EE-HHHHHHHHHHHH
T ss_pred CcCCCCCCCCCHHHHHHHHHHHH
Confidence 378888777654 4555543
No 74
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=51.38 E-value=7.4 Score=30.94 Aligned_cols=36 Identities=19% Similarity=0.424 Sum_probs=21.4
Q ss_pred cceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 42 r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
.-+|.||+|+.+--...+ ..-..---.++|-+|-..
T Consensus 20 ~k~FtCp~Cghe~vs~ct-----vkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCT-----VKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred CceEecCccCCeeeeEEE-----EEecCceeEEEcccCcce
Confidence 458999999975322222 111122334689999876
No 75
>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=50.98 E-value=6.2 Score=30.92 Aligned_cols=30 Identities=23% Similarity=0.269 Sum_probs=23.2
Q ss_pred CccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
+.+..+.|+-|+..+..... ...||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 45788999999987766533 3679999874
No 76
>PRK12495 hypothetical protein; Provisional
Probab=50.90 E-value=8.8 Score=34.21 Aligned_cols=31 Identities=19% Similarity=0.411 Sum_probs=22.5
Q ss_pred cceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccch
Q 028989 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (200)
Q Consensus 42 r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~ 85 (200)
...|.||.|+..+- .. ...++||+|-..+..
T Consensus 40 msa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGDPIF------------RH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccCccc------------CC-CCeeECCCCCCcccc
Confidence 34689999999733 12 445789999988764
No 77
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=50.75 E-value=7.1 Score=37.77 Aligned_cols=61 Identities=18% Similarity=0.348 Sum_probs=35.7
Q ss_pred CCCCCCCCCccceecCCCCccc---ccHHHHHhhhhhcCCCCCCcccccccccc--------cc---hhhhhhhhhhccc
Q 028989 32 YDETDGDDDLNAMFLCPFCAED---FDIVGLCCHIDEDHPIEAKNGVCPVCAKR--------VG---TDIVSHITMQHGN 97 (200)
Q Consensus 32 ~ee~e~d~d~r~~F~CPfC~e~---fD~~~Lc~H~~~eH~~e~k~vVCPICa~~--------v~---~d~v~Hlt~qH~~ 97 (200)
+++.+.++..++.|.||+|... +|...|..- +...-.|-.|-.- .+ ...+++++-|--.
T Consensus 116 led~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~-------~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~~~~Q~~p 188 (436)
T KOG2593|consen 116 LEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDN-------ETGEFHCENCGGELVEDENKLPSKESRTALNRLMEQLEP 188 (436)
T ss_pred HHHHhhhccccccccCCccccchhhhHHHHhhcc-------cCceEEEecCCCchhcccccCchHHHHHHHHHHHHHHHH
Confidence 3343345567899999999985 555555442 1233567777653 22 2455666555444
Q ss_pred hh
Q 028989 98 FF 99 (200)
Q Consensus 98 ~~ 99 (200)
++
T Consensus 189 i~ 190 (436)
T KOG2593|consen 189 II 190 (436)
T ss_pred HH
Confidence 43
No 78
>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=50.49 E-value=11 Score=24.06 Aligned_cols=18 Identities=28% Similarity=0.757 Sum_probs=9.4
Q ss_pred ccccccccccc-hhhhhhh
Q 028989 74 GVCPVCAKRVG-TDIVSHI 91 (200)
Q Consensus 74 vVCPICa~~v~-~d~v~Hl 91 (200)
+.||.|...|. .-|+.||
T Consensus 5 ~~C~nC~R~v~a~RfA~HL 23 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAPHL 23 (33)
T ss_dssp EE-TTTSSEEEGGGHHHHH
T ss_pred EECCCCcCCcchhhhHHHH
Confidence 45666666544 3566665
No 79
>PF13395 HNH_4: HNH endonuclease
Probab=50.29 E-value=8.1 Score=26.24 Aligned_cols=13 Identities=38% Similarity=1.145 Sum_probs=11.3
Q ss_pred CCCCcccccHHHH
Q 028989 47 CPFCAEDFDIVGL 59 (200)
Q Consensus 47 CPfC~e~fD~~~L 59 (200)
||||++.++...|
T Consensus 1 C~Y~g~~i~~~~l 13 (54)
T PF13395_consen 1 CPYCGKPISIENL 13 (54)
T ss_pred CCCCCCCCChhhc
Confidence 8999999888876
No 80
>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=50.22 E-value=5.3 Score=30.92 Aligned_cols=15 Identities=33% Similarity=0.897 Sum_probs=11.5
Q ss_pred CCccceecCCCCccc
Q 028989 39 DDLNAMFLCPFCAED 53 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~ 53 (200)
..+.+.|.||||+..
T Consensus 30 ~~q~~ky~Cp~Cgk~ 44 (90)
T PF01780_consen 30 ISQHAKYTCPFCGKT 44 (90)
T ss_dssp HHHHS-BEESSSSSS
T ss_pred HHHhCCCcCCCCCCc
Confidence 456789999999985
No 81
>PF15616 TerY-C: TerY-C metal binding domain
Probab=49.95 E-value=4.8 Score=32.99 Aligned_cols=43 Identities=16% Similarity=0.288 Sum_probs=30.6
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCC-CCCcccccccccccchhhh
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPI-EAKNGVCPVCAKRVGTDIV 88 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~-e~k~vVCPICa~~v~~d~v 88 (200)
.=.||+|+..+-.+.. =|-.-|+. ....++||-|-.......+
T Consensus 77 ~PgCP~CGn~~~fa~C--~CGkl~Ci~g~~~~~CPwCg~~g~~~~~ 120 (131)
T PF15616_consen 77 APGCPHCGNQYAFAVC--GCGKLFCIDGEGEVTCPWCGNEGSFGAG 120 (131)
T ss_pred CCCCCCCcChhcEEEe--cCCCEEEeCCCCCEECCCCCCeeeeccc
Confidence 3589999987555433 47777885 4456899999987655444
No 82
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.92 E-value=9.8 Score=22.44 Aligned_cols=9 Identities=33% Similarity=1.246 Sum_probs=6.0
Q ss_pred cCCCCcccc
Q 028989 46 LCPFCAEDF 54 (200)
Q Consensus 46 ~CPfC~e~f 54 (200)
.||.|+..+
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 577777644
No 83
>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=49.69 E-value=7.4 Score=30.59 Aligned_cols=37 Identities=32% Similarity=0.673 Sum_probs=23.6
Q ss_pred cCCCCccc---ccHHHHHhhhhhcCCCCCCcccccccccccch
Q 028989 46 LCPFCAED---FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (200)
Q Consensus 46 ~CPfC~e~---fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~ 85 (200)
.||||+.. .+-..+.-|-.++++. .-+|+-|-+.||.
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 69999985 3433444433333321 2699999999874
No 84
>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=49.66 E-value=11 Score=22.08 Aligned_cols=22 Identities=41% Similarity=0.644 Sum_probs=15.1
Q ss_pred HHhhhhhcCCCCCCcccccccccc
Q 028989 59 LCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 59 Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
|..|+.. |..+ ++-.||+|...
T Consensus 2 l~~H~~~-H~~~-k~~~C~~C~k~ 23 (26)
T PF13465_consen 2 LRRHMRT-HTGE-KPYKCPYCGKS 23 (26)
T ss_dssp HHHHHHH-HSSS-SSEEESSSSEE
T ss_pred HHHHhhh-cCCC-CCCCCCCCcCe
Confidence 6677775 5544 66788888754
No 85
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=48.99 E-value=10 Score=30.21 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=22.1
Q ss_pred cccccccccc-----cchhhhhhhhhhccchhh
Q 028989 73 NGVCPVCAKR-----VGTDIVSHITMQHGNFFK 100 (200)
Q Consensus 73 ~vVCPICa~~-----v~~d~v~Hlt~qH~~~~K 100 (200)
.|.||+|... .......||+.-||-.-.
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s~ 57 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISST 57 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhccccccC
Confidence 7899999954 345789999999998654
No 86
>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=48.77 E-value=10 Score=22.86 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=5.3
Q ss_pred cCCCCcccc
Q 028989 46 LCPFCAEDF 54 (200)
Q Consensus 46 ~CPfC~e~f 54 (200)
.||-|+..+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 366666654
No 87
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=48.38 E-value=5.9 Score=28.76 Aligned_cols=26 Identities=31% Similarity=0.675 Sum_probs=19.2
Q ss_pred cccccccc--cchhhhhhhhhhccchhh
Q 028989 75 VCPVCAKR--VGTDIVSHITMQHGNFFK 100 (200)
Q Consensus 75 VCPICa~~--v~~d~v~Hlt~qH~~~~K 100 (200)
-||-|.+. -.+|.+.|.+-.|+++|-
T Consensus 19 rCPRC~~~FR~~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 19 RCPRCGMVFRRRKDYIRHVNKAHGWLFG 46 (65)
T ss_pred eCCchhHHHHHhHHHHHHhhHHhhhhhc
Confidence 46666554 456899999999999873
No 88
>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=47.45 E-value=15 Score=29.98 Aligned_cols=41 Identities=29% Similarity=0.674 Sum_probs=30.0
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccchhhh
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDIV 88 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d~v 88 (200)
....|.-|+..++...+...+..... ..||.|...+-.|.+
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~~-----~~C~~C~~~lrp~vv 144 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEEP-----PRCPKCGGLLRPDVV 144 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTSS-----CBCTTTSCBEEEEE-
T ss_pred ceeeecCCCccccchhhccccccccc-----ccccccCccCCCCee
Confidence 36899999999888877766655533 299999997555443
No 89
>PF14279 HNH_5: HNH endonuclease
Probab=47.41 E-value=6.6 Score=28.68 Aligned_cols=44 Identities=20% Similarity=0.567 Sum_probs=26.6
Q ss_pred CCCCcccccHHHH-HhhhhhcC---CCCCCcccccccccccchhhhhhh
Q 028989 47 CPFCAEDFDIVGL-CCHIDEDH---PIEAKNGVCPVCAKRVGTDIVSHI 91 (200)
Q Consensus 47 CPfC~e~fD~~~L-c~H~~~eH---~~e~k~vVCPICa~~v~~d~v~Hl 91 (200)
|.||.++.+.... .+|+--+= ....+. ||-.|-..+|...-+++
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN-VCDKCNNKFGSKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc-hhHHHhHHHhHHHHHHH
Confidence 8999997655432 23333221 123344 99999998876555555
No 90
>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=46.37 E-value=8.6 Score=30.81 Aligned_cols=25 Identities=24% Similarity=0.792 Sum_probs=15.0
Q ss_pred cCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
+||-|..++.-. +....|||-|+--
T Consensus 4 ~CP~C~seytY~------------dg~~~iCpeC~~E 28 (109)
T TIGR00686 4 PCPKCNSEYTYH------------DGTQLICPSCLYE 28 (109)
T ss_pred cCCcCCCcceEe------------cCCeeECcccccc
Confidence 678776653211 3344688888764
No 91
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=46.25 E-value=13 Score=31.61 Aligned_cols=25 Identities=32% Similarity=0.942 Sum_probs=17.9
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
.+.||-||-- |-. -.+.+||||-+.
T Consensus 134 ~~vC~vCGy~-------------~~g-e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYT-------------HEG-EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCc-------------ccC-CCCCcCCCCCCh
Confidence 8999999742 112 335799999875
No 92
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=45.83 E-value=8.8 Score=25.12 Aligned_cols=28 Identities=25% Similarity=0.483 Sum_probs=16.2
Q ss_pred cCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
.||-|+..+-...+ + .....|||.|...
T Consensus 2 FCp~Cg~~l~~~~~------~---~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEG------K---EKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccC------C---CCCEEECCcCCCe
Confidence 58888875432211 1 1125789999754
No 93
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.73 E-value=13 Score=37.74 Aligned_cols=29 Identities=34% Similarity=0.469 Sum_probs=24.5
Q ss_pred cceecCCCCcc-cccHHHHHhhhhhcCCCC
Q 028989 42 NAMFLCPFCAE-DFDIVGLCCHIDEDHPIE 70 (200)
Q Consensus 42 r~~F~CPfC~e-~fD~~~Lc~H~~~eH~~e 70 (200)
+.--.|+||.+ .||..+|..|+..+|.+.
T Consensus 180 rGhp~C~~C~~~fld~~el~rH~~~~h~~c 209 (669)
T KOG2231|consen 180 RGHPLCKFCHERFLDDDELYRHLRFDHEFC 209 (669)
T ss_pred cCCccchhhhhhhccHHHHHHhhccceehe
Confidence 33568999999 499999999999999863
No 94
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=45.53 E-value=7 Score=22.79 Aligned_cols=7 Identities=43% Similarity=1.460 Sum_probs=3.6
Q ss_pred CCCCccc
Q 028989 47 CPFCAED 53 (200)
Q Consensus 47 CPfC~e~ 53 (200)
||.|+.+
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 5555543
No 95
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=44.46 E-value=12 Score=31.15 Aligned_cols=33 Identities=33% Similarity=0.736 Sum_probs=19.5
Q ss_pred cCCCCcccccHHHHHhhhhhcCCCCCCc-----ccccccccccc
Q 028989 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKN-----GVCPVCAKRVG 84 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~~~eH~~e~k~-----vVCPICa~~v~ 84 (200)
.||||+.... |+.+.-.....| --||-|....+
T Consensus 2 ~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCcce
Confidence 6999997431 233333333333 34999998744
No 96
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=43.64 E-value=18 Score=23.22 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=7.9
Q ss_pred CCcccccccc
Q 028989 71 AKNGVCPVCA 80 (200)
Q Consensus 71 ~k~vVCPICa 80 (200)
.+.++||+|.
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 5678899985
No 97
>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=42.87 E-value=7.5 Score=30.26 Aligned_cols=30 Identities=23% Similarity=0.504 Sum_probs=19.8
Q ss_pred CccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
..+..+.|+-|+.+|+..... ..||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~-------------~~CP~Cgs~ 95 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFD-------------FSCPRCGSP 95 (113)
T ss_dssp EE--EEEETTTS-EEECHHCC-------------HH-SSSSSS
T ss_pred ecCCcEECCCCCCEEecCCCC-------------CCCcCCcCC
Confidence 457899999999988766543 239999875
No 98
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=42.67 E-value=13 Score=35.23 Aligned_cols=40 Identities=33% Similarity=0.593 Sum_probs=31.6
Q ss_pred eecCCC--Ccc-cccHHHHHhhhhhcCC-----------------CCCCccccccccccc
Q 028989 44 MFLCPF--CAE-DFDIVGLCCHIDEDHP-----------------IEAKNGVCPVCAKRV 83 (200)
Q Consensus 44 ~F~CPf--C~e-~fD~~~Lc~H~~~eH~-----------------~e~k~vVCPICa~~v 83 (200)
-|.||. |.+ .-.+-+|--|...-|+ .+.|+.+|+||.++.
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhh
Confidence 388986 777 4788999999998883 244778899999874
No 99
>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=42.54 E-value=19 Score=21.47 Aligned_cols=21 Identities=24% Similarity=0.668 Sum_probs=13.0
Q ss_pred eecCCCCccccc-HHHHHhhhh
Q 028989 44 MFLCPFCAEDFD-IVGLCCHID 64 (200)
Q Consensus 44 ~F~CPfC~e~fD-~~~Lc~H~~ 64 (200)
.|.|..|+..|. ...+-.|+.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 356777777644 566666654
No 100
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=41.82 E-value=11 Score=29.50 Aligned_cols=30 Identities=23% Similarity=0.431 Sum_probs=22.0
Q ss_pred CccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
+.+..+.|+-|+..|.... ....||.|...
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 5678899999998765543 23469999864
No 101
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=40.16 E-value=8.2 Score=29.94 Aligned_cols=15 Identities=27% Similarity=0.758 Sum_probs=12.4
Q ss_pred CCccceecCCCCccc
Q 028989 39 DDLNAMFLCPFCAED 53 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~ 53 (200)
.-+.+.|.|+||++.
T Consensus 31 i~Qhaky~CsfCGK~ 45 (92)
T KOG0402|consen 31 IQQHAKYTCSFCGKK 45 (92)
T ss_pred HHHhhhhhhhhcchh
Confidence 356789999999985
No 102
>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=40.11 E-value=12 Score=25.91 Aligned_cols=45 Identities=16% Similarity=0.273 Sum_probs=28.0
Q ss_pred CCCCCCC-CCccceecCCCCccc--ccHHHHHhhhhhcCCCCCCcccccccccccch
Q 028989 32 YDETDGD-DDLNAMFLCPFCAED--FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGT 85 (200)
Q Consensus 32 ~ee~e~d-~d~r~~F~CPfC~e~--fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~ 85 (200)
+++++.+ ++..-+|+|+ ||-. +....|-.+ .--+.|+-|+-.|..
T Consensus 5 l~d~~~~~~~~~~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~V 52 (55)
T PF05207_consen 5 LDDMEFDEEEGVYSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIRV 52 (55)
T ss_dssp TTTSEEETTTTEEEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEEE
T ss_pred hhhceecCCCCEEEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEEE
Confidence 3444332 2345789995 9975 666776555 334679999987543
No 103
>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=40.10 E-value=17 Score=25.03 Aligned_cols=14 Identities=36% Similarity=0.980 Sum_probs=11.4
Q ss_pred CccceecCCCCccc
Q 028989 40 DLNAMFLCPFCAED 53 (200)
Q Consensus 40 d~r~~F~CPfC~e~ 53 (200)
++..+|.||-|+..
T Consensus 30 ~Lp~~w~CP~C~a~ 43 (50)
T cd00730 30 DLPDDWVCPVCGAG 43 (50)
T ss_pred HCCCCCCCCCCCCc
Confidence 57788999999873
No 104
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=39.89 E-value=13 Score=29.28 Aligned_cols=9 Identities=44% Similarity=1.527 Sum_probs=7.6
Q ss_pred eecCCCCcc
Q 028989 44 MFLCPFCAE 52 (200)
Q Consensus 44 ~F~CPfC~e 52 (200)
..+||||++
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 468999998
No 105
>PRK03922 hypothetical protein; Provisional
Probab=39.77 E-value=13 Score=29.93 Aligned_cols=16 Identities=38% Similarity=0.847 Sum_probs=12.2
Q ss_pred eecCCCCcccccHHHH
Q 028989 44 MFLCPFCAEDFDIVGL 59 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~L 59 (200)
.-.||+|+++||-+.+
T Consensus 49 ~~~cP~cge~~~~afv 64 (113)
T PRK03922 49 LTICPKCGEPFDSAFV 64 (113)
T ss_pred cccCCCCCCcCCcEEE
Confidence 4589999999885543
No 106
>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=39.64 E-value=16 Score=23.23 Aligned_cols=27 Identities=22% Similarity=0.552 Sum_probs=14.2
Q ss_pred cceecCCCCcccccH-----HHHHhhhhhcCC
Q 028989 42 NAMFLCPFCAEDFDI-----VGLCCHIDEDHP 68 (200)
Q Consensus 42 r~~F~CPfC~e~fD~-----~~Lc~H~~~eH~ 68 (200)
.....|-||+..+.. ..|..|+...||
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~hp 45 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKHP 45 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTTH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhCc
Confidence 345577777775544 366666655553
No 107
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.48 E-value=15 Score=29.58 Aligned_cols=18 Identities=17% Similarity=0.612 Sum_probs=14.1
Q ss_pred CccceecCCCCcccccHH
Q 028989 40 DLNAMFLCPFCAEDFDIV 57 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD~~ 57 (200)
..+..+.|+-|+..+...
T Consensus 66 ~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred ecceEEECCCCCCEEecc
Confidence 556899999999876554
No 108
>smart00507 HNHc HNH nucleases.
Probab=39.35 E-value=5.8 Score=24.59 Aligned_cols=21 Identities=19% Similarity=0.216 Sum_probs=13.5
Q ss_pred ecCCCCcccccHHHHHhhhhh
Q 028989 45 FLCPFCAEDFDIVGLCCHIDE 65 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~ 65 (200)
+.|++|+..++...-+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 689999987654333445543
No 109
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=38.81 E-value=14 Score=29.31 Aligned_cols=16 Identities=31% Similarity=0.694 Sum_probs=12.2
Q ss_pred eecCCCCcccccHHHH
Q 028989 44 MFLCPFCAEDFDIVGL 59 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~L 59 (200)
.-.||+|+++++-+.+
T Consensus 47 ~~~cP~Cge~~~~a~v 62 (102)
T PF04475_consen 47 DTICPKCGEELDSAFV 62 (102)
T ss_pred cccCCCCCCccCceEE
Confidence 4589999999885543
No 110
>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=38.69 E-value=15 Score=35.78 Aligned_cols=29 Identities=28% Similarity=0.590 Sum_probs=23.4
Q ss_pred Ccccccccccccc--hhhhhhhhhhccchhh
Q 028989 72 KNGVCPVCAKRVG--TDIVSHITMQHGNFFK 100 (200)
Q Consensus 72 k~vVCPICa~~v~--~d~v~Hlt~qH~~~~K 100 (200)
+.-+||+|..+.. .++..|+-.+|-.-++
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 3456999998754 5999999999988774
No 111
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.20 E-value=14 Score=29.62 Aligned_cols=37 Identities=30% Similarity=0.483 Sum_probs=23.2
Q ss_pred cceecCCCCcccccHH-HH------HhhhhhcCCCCCCcccccccc
Q 028989 42 NAMFLCPFCAEDFDIV-GL------CCHIDEDHPIEAKNGVCPVCA 80 (200)
Q Consensus 42 r~~F~CPfC~e~fD~~-~L------c~H~~~eH~~e~k~vVCPICa 80 (200)
...+.||.|.+.|... .| |..|...... ....||+|.
T Consensus 11 ~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~--~~~~Cp~cr 54 (386)
T KOG2177|consen 11 QEELTCPICLEYFREPVLLPCGHNFCRACLTRSWE--GPLSCPVCR 54 (386)
T ss_pred cccccChhhHHHhhcCccccccchHhHHHHHHhcC--CCcCCcccC
Confidence 3467999999876655 22 2333333322 347899999
No 112
>PRK11595 DNA utilization protein GntX; Provisional
Probab=37.65 E-value=19 Score=30.84 Aligned_cols=34 Identities=24% Similarity=0.609 Sum_probs=18.5
Q ss_pred cCCCCcccccH--HHHHhhhhhcCCCCCCccccccccc
Q 028989 46 LCPFCAEDFDI--VGLCCHIDEDHPIEAKNGVCPVCAK 81 (200)
Q Consensus 46 ~CPfC~e~fD~--~~Lc~H~~~eH~~e~k~vVCPICa~ 81 (200)
.|+.|++.+.. ..||.+|.+.=+.- ...||.|..
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg~ 42 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCGL 42 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCCC
Confidence 37777765432 35777776552221 235666654
No 113
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=37.64 E-value=19 Score=33.90 Aligned_cols=40 Identities=33% Similarity=0.680 Sum_probs=30.2
Q ss_pred ceecCCCCccccc--HHHHHhhhhhc-CCC-----CCCcccccccccc
Q 028989 43 AMFLCPFCAEDFD--IVGLCCHIDED-HPI-----EAKNGVCPVCAKR 82 (200)
Q Consensus 43 ~~F~CPfC~e~fD--~~~Lc~H~~~e-H~~-----e~k~vVCPICa~~ 82 (200)
.+-.||.||...| +.+||.=|--+ |+. +.+-.+|+.|-+.
T Consensus 5 ~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~ 52 (355)
T COG1499 5 STILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGAY 52 (355)
T ss_pred cccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCCc
Confidence 3568999999988 88999877666 554 3344689999864
No 114
>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=37.39 E-value=11 Score=32.28 Aligned_cols=21 Identities=14% Similarity=0.585 Sum_probs=0.0
Q ss_pred ccccccccccc-hhhhhhhhhh
Q 028989 74 GVCPVCAKRVG-TDIVSHITMQ 94 (200)
Q Consensus 74 vVCPICa~~v~-~d~v~Hlt~q 94 (200)
.+||||..+|- ..|-.||++.
T Consensus 169 ~~cPitGe~IP~~e~~eHmRi~ 190 (229)
T PF12230_consen 169 IICPITGEMIPADEMDEHMRIE 190 (229)
T ss_dssp ----------------------
T ss_pred cccccccccccccccccccccc
Confidence 68999999966 5899999653
No 115
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=36.91 E-value=26 Score=19.44 Aligned_cols=20 Identities=25% Similarity=0.547 Sum_probs=9.3
Q ss_pred ecCCCCccc-ccHHHHHhhhh
Q 028989 45 FLCPFCAED-FDIVGLCCHID 64 (200)
Q Consensus 45 F~CPfC~e~-fD~~~Lc~H~~ 64 (200)
|.|..|... -+...|..|+.
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 345555443 44444444443
No 116
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=35.94 E-value=24 Score=23.40 Aligned_cols=27 Identities=22% Similarity=0.552 Sum_probs=18.4
Q ss_pred ceecCCCCcccccHH------HHHhhhhhcCCC
Q 028989 43 AMFLCPFCAEDFDIV------GLCCHIDEDHPI 69 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~------~Lc~H~~~eH~~ 69 (200)
+.-.|-+|+..+... .|..|+...|+.
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~ 49 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHPA 49 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCcC
Confidence 566788888865543 677777766653
No 117
>PRK00420 hypothetical protein; Validated
Probab=35.92 E-value=24 Score=28.16 Aligned_cols=27 Identities=30% Similarity=0.551 Sum_probs=18.0
Q ss_pred ecCCCCcccccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
-.||.|+..+= . .-...++||+|..-+
T Consensus 24 ~~CP~Cg~pLf--~----------lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLF--E----------LKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcce--e----------cCCCceECCCCCCee
Confidence 48999986521 1 113457999999863
No 118
>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=35.61 E-value=12 Score=32.00 Aligned_cols=23 Identities=22% Similarity=0.427 Sum_probs=0.0
Q ss_pred eecCCCCcccccHHHHHhhhhhc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDED 66 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~e 66 (200)
...||.||+.+-+..+-.|+..+
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi~ 190 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRIE 190 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 47999999999999999999876
No 119
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=35.50 E-value=25 Score=35.55 Aligned_cols=54 Identities=26% Similarity=0.481 Sum_probs=35.7
Q ss_pred CCCccceecCCCCccc-cc-HHHHHhh-----hh---hcCCCCCCcccccccccccchhhhhhh
Q 028989 38 DDDLNAMFLCPFCAED-FD-IVGLCCH-----ID---EDHPIEAKNGVCPVCAKRVGTDIVSHI 91 (200)
Q Consensus 38 d~d~r~~F~CPfC~e~-fD-~~~Lc~H-----~~---~eH~~e~k~vVCPICa~~v~~d~v~Hl 91 (200)
.+|...+-.|-+|... =| +..=|.| |. .+--.+..+|.||+|...++-|+.+|-
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 4567778899999873 22 2233333 22 234457788999999998887766663
No 120
>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=35.40 E-value=19 Score=33.43 Aligned_cols=37 Identities=24% Similarity=0.460 Sum_probs=23.6
Q ss_pred ecCCCCccc--ccHH----------HHHhhhhhcCCCCCCcccccccccc
Q 028989 45 FLCPFCAED--FDIV----------GLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 45 F~CPfC~e~--fD~~----------~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
+.||.|..+ +.-. .+|..|.+..-. ...+.||+|...
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~-~~~~~CP~C~~~ 52 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV-RGSGSCPECDTP 52 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc-CCCCCCCCCCCc
Confidence 589999873 2211 346666666532 345689999775
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=34.79 E-value=17 Score=35.52 Aligned_cols=43 Identities=26% Similarity=0.512 Sum_probs=27.0
Q ss_pred cceecCCCCcccccH--HHHHhhhhhcCCCCCCcccccccccccchh
Q 028989 42 NAMFLCPFCAEDFDI--VGLCCHIDEDHPIEAKNGVCPVCAKRVGTD 86 (200)
Q Consensus 42 r~~F~CPfC~e~fD~--~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d 86 (200)
+-..+||-|++.+.+ ..|.- +++...+.--.+||-|...+...
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w--~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKW--DKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred EEEccCCCCCCCccccccceee--cCCCCccceEEECCCCcCCCCHH
Confidence 456899999996443 33322 22223334446899999988753
No 122
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=34.08 E-value=23 Score=36.96 Aligned_cols=52 Identities=29% Similarity=0.459 Sum_probs=37.1
Q ss_pred CccceecCCCCcccccHH-HHHhhhhhcCCCCCCcccccccccccc--hhhhhhhhh
Q 028989 40 DLNAMFLCPFCAEDFDIV-GLCCHIDEDHPIEAKNGVCPVCAKRVG--TDIVSHITM 93 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD~~-~Lc~H~~~eH~~e~k~vVCPICa~~v~--~d~v~Hlt~ 93 (200)
..--.|.|+-|++-|-.. -|-+|++.+ ..-|+--||-|-++.+ ..+-.||+.
T Consensus 277 a~lRKFKCtECgKAFKfKHHLKEHlRIH--SGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 277 ALLRKFKCTECGKAFKFKHHLKEHLRIH--SGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred hhhccccccccchhhhhHHHHHhhheee--cCCCCcCCcccccccccCCcccccccc
Confidence 445589999999976543 466666654 3457788999999965 577777753
No 123
>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=33.96 E-value=25 Score=28.91 Aligned_cols=34 Identities=21% Similarity=0.528 Sum_probs=24.3
Q ss_pred CccceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccccchh
Q 028989 40 DLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTD 86 (200)
Q Consensus 40 d~r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d 86 (200)
|+-....||-|+.- ||+ ...++|||-|..-+...
T Consensus 5 elGtKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDL-------------NRRPAVSPYTGEQFPPE 39 (129)
T ss_pred hhCccccCCCcCcccccc-------------CCCCccCCCcCCccCcc
Confidence 45567899999985 663 23578999998765444
No 124
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.59 E-value=24 Score=33.36 Aligned_cols=21 Identities=33% Similarity=0.996 Sum_probs=18.7
Q ss_pred ecCCCCcccccHHHHHhhhhh
Q 028989 45 FLCPFCAEDFDIVGLCCHIDE 65 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~ 65 (200)
--||||.-.+.....|.|++.
T Consensus 3 ~iCP~CkLsv~~~~m~~Hiea 23 (393)
T KOG4696|consen 3 IICPFCKLSVNYDEMCFHIEA 23 (393)
T ss_pred ccccceecccCHHHHHHHHHh
Confidence 469999988999999999984
No 125
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=33.22 E-value=21 Score=32.17 Aligned_cols=16 Identities=25% Similarity=0.810 Sum_probs=9.2
Q ss_pred eecCCCCcccccHHHH
Q 028989 44 MFLCPFCAEDFDIVGL 59 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~L 59 (200)
.|+|-.|++-|..+-+
T Consensus 117 ~ftCrvCgK~F~lQRm 132 (267)
T KOG3576|consen 117 SFTCRVCGKKFGLQRM 132 (267)
T ss_pred eeeeehhhhhhhHHHH
Confidence 4666666666555543
No 126
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=33.16 E-value=24 Score=24.85 Aligned_cols=36 Identities=28% Similarity=0.644 Sum_probs=22.4
Q ss_pred ecCCCCcccccHHHHHhhhh------------------hcCCCCCCccccccccc
Q 028989 45 FLCPFCAEDFDIVGLCCHID------------------EDHPIEAKNGVCPVCAK 81 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~------------------~eH~~e~k~vVCPICa~ 81 (200)
-.||+|.-.+|...|..=.. +.|..+ ...+||.|..
T Consensus 8 L~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~e-g~L~Cp~c~r 61 (68)
T PF03966_consen 8 LACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVE-GELICPECGR 61 (68)
T ss_dssp BB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTT-TEEEETTTTE
T ss_pred hcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccC-CEEEcCCCCC
Confidence 47999988787777765221 123333 4578999964
No 127
>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=32.95 E-value=25 Score=21.65 Aligned_cols=18 Identities=22% Similarity=0.519 Sum_probs=9.7
Q ss_pred HHHHhhhhhcCCCCCCccccccc
Q 028989 57 VGLCCHIDEDHPIEAKNGVCPVC 79 (200)
Q Consensus 57 ~~Lc~H~~~eH~~e~k~vVCPIC 79 (200)
.-|..+++. .....||+|
T Consensus 24 ~C~~~~~~~-----~~~~~CP~C 41 (41)
T PF00097_consen 24 DCLRKWLEN-----SGSVKCPLC 41 (41)
T ss_dssp HHHHHHHHH-----TSSSBTTTT
T ss_pred HHHHHHHHh-----cCCccCCcC
Confidence 334444444 444567776
No 128
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=32.77 E-value=41 Score=32.46 Aligned_cols=38 Identities=29% Similarity=0.551 Sum_probs=23.8
Q ss_pred eecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 44 MFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 44 ~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
.|+||.|+-- =-.++|-.|+.-.|.- .|.--|--|..+
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~ 301 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTR 301 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhh
Confidence 4667777654 4456666777766665 566666666665
No 129
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.53 E-value=20 Score=38.36 Aligned_cols=38 Identities=21% Similarity=0.488 Sum_probs=22.4
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccc
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVG 84 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~ 84 (200)
..|.||.|+..-...--|..|... .....||-|-..+.
T Consensus 637 ~~frCP~CG~~Te~i~fCP~CG~~----~~~y~CPKCG~El~ 674 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRCGIE----VEEDECEKCGREPT 674 (1121)
T ss_pred CcccCCCCCCCCCcceeCccccCc----CCCCcCCCCCCCCC
Confidence 456777777654444556666322 33456888877643
No 130
>PRK10220 hypothetical protein; Provisional
Probab=31.96 E-value=26 Score=28.23 Aligned_cols=10 Identities=40% Similarity=0.966 Sum_probs=6.5
Q ss_pred cccccccccc
Q 028989 73 NGVCPVCAKR 82 (200)
Q Consensus 73 ~vVCPICa~~ 82 (200)
..|||-|+--
T Consensus 20 ~~vCpeC~hE 29 (111)
T PRK10220 20 MYICPECAHE 29 (111)
T ss_pred eEECCcccCc
Confidence 4577777653
No 131
>PF14353 CpXC: CpXC protein
Probab=31.78 E-value=22 Score=27.55 Aligned_cols=13 Identities=38% Similarity=0.971 Sum_probs=10.6
Q ss_pred ceecCCCCccccc
Q 028989 43 AMFLCPFCAEDFD 55 (200)
Q Consensus 43 ~~F~CPfC~e~fD 55 (200)
-.|.||.|+..+-
T Consensus 37 ~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 37 FSFTCPSCGHKFR 49 (128)
T ss_pred CEEECCCCCCcee
Confidence 4799999999743
No 132
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=30.91 E-value=17 Score=24.05 Aligned_cols=11 Identities=27% Similarity=1.222 Sum_probs=8.6
Q ss_pred eecCCCCcccc
Q 028989 44 MFLCPFCAEDF 54 (200)
Q Consensus 44 ~F~CPfC~e~f 54 (200)
.-.||||+..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 56999998753
No 133
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.91 E-value=22 Score=34.09 Aligned_cols=15 Identities=27% Similarity=0.747 Sum_probs=11.4
Q ss_pred cceecCCCCcccccH
Q 028989 42 NAMFLCPFCAEDFDI 56 (200)
Q Consensus 42 r~~F~CPfC~e~fD~ 56 (200)
..+|.||||..+-+.
T Consensus 372 ~~sfKCPYCP~e~~~ 386 (394)
T KOG2817|consen 372 SQSFKCPYCPVEQLA 386 (394)
T ss_pred CeeeeCCCCCcccCH
Confidence 457999999887544
No 134
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=30.44 E-value=38 Score=28.99 Aligned_cols=31 Identities=29% Similarity=0.634 Sum_probs=22.7
Q ss_pred ccceecCCCCccc--ccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 41 LNAMFLCPFCAED--FDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 41 ~r~~F~CPfC~e~--fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
....|.||-|..- ||.+.+.. -.||.|-+.+
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~~~------------F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAMELG------------FTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCcccHHHHHHhC------------CCCCCCCchh
Confidence 3457999999884 66655433 6899999874
No 135
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=30.37 E-value=13 Score=29.83 Aligned_cols=13 Identities=31% Similarity=0.981 Sum_probs=9.6
Q ss_pred CCCCcccccHHHH
Q 028989 47 CPFCAEDFDIVGL 59 (200)
Q Consensus 47 CPfC~e~fD~~~L 59 (200)
||-|+..+-+..|
T Consensus 1 CPvCg~~l~vt~l 13 (113)
T PF09862_consen 1 CPVCGGELVVTRL 13 (113)
T ss_pred CCCCCCceEEEEE
Confidence 8999887766554
No 136
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=30.01 E-value=23 Score=33.53 Aligned_cols=12 Identities=42% Similarity=1.018 Sum_probs=10.1
Q ss_pred cceecCCCCccc
Q 028989 42 NAMFLCPFCAED 53 (200)
Q Consensus 42 r~~F~CPfC~e~ 53 (200)
..+|.||||.++
T Consensus 374 ~~~FKCPYCP~~ 385 (396)
T COG5109 374 VLSFKCPYCPEM 385 (396)
T ss_pred cEEeeCCCCCcc
Confidence 458999999885
No 137
>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=29.84 E-value=25 Score=24.43 Aligned_cols=9 Identities=33% Similarity=1.409 Sum_probs=8.2
Q ss_pred eecCCCCcc
Q 028989 44 MFLCPFCAE 52 (200)
Q Consensus 44 ~F~CPfC~e 52 (200)
.|.||+|+.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 899999985
No 138
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.28 E-value=14 Score=34.20 Aligned_cols=42 Identities=31% Similarity=0.505 Sum_probs=26.4
Q ss_pred cceecCCCCccc--ccHHHH-HhhhhhcCCCCCCc-----cccccccccc
Q 028989 42 NAMFLCPFCAED--FDIVGL-CCHIDEDHPIEAKN-----GVCPVCAKRV 83 (200)
Q Consensus 42 r~~F~CPfC~e~--fD~~~L-c~H~~~eH~~e~k~-----vVCPICa~~v 83 (200)
..+-.||+|++. +--... |.|+-=.-|.-++- -.||-|.+.+
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 345689999995 444444 88855444443333 2688888764
No 139
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.11 E-value=26 Score=24.89 Aligned_cols=13 Identities=31% Similarity=0.649 Sum_probs=10.2
Q ss_pred ccceecCCCCccc
Q 028989 41 LNAMFLCPFCAED 53 (200)
Q Consensus 41 ~r~~F~CPfC~e~ 53 (200)
.+..|.||.||.-
T Consensus 11 ~~v~~~Cp~cGip 23 (55)
T PF13824_consen 11 AHVNFECPDCGIP 23 (55)
T ss_pred cccCCcCCCCCCc
Confidence 3568999999764
No 140
>PF14968 CCDC84: Coiled coil protein 84
Probab=28.84 E-value=28 Score=32.62 Aligned_cols=26 Identities=23% Similarity=0.478 Sum_probs=19.6
Q ss_pred CCccceecCCCCcccccHH-------HHHhhhh
Q 028989 39 DDLNAMFLCPFCAEDFDIV-------GLCCHID 64 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~fD~~-------~Lc~H~~ 64 (200)
.+.+..|=|+||+.+++.. ++..|+-
T Consensus 53 ~~~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLa 85 (336)
T PF14968_consen 53 PEHRNRFWCVFCDCEVREHDSSFACGGAIEHLA 85 (336)
T ss_pred ccccceeEeeCccchhhhccchhhhccHHhhcC
Confidence 4667899999999986655 6666664
No 141
>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=27.66 E-value=14 Score=30.65 Aligned_cols=14 Identities=14% Similarity=0.230 Sum_probs=11.0
Q ss_pred CccceecCCCCccc
Q 028989 40 DLNAMFLCPFCAED 53 (200)
Q Consensus 40 d~r~~F~CPfC~e~ 53 (200)
|....|.||||+.-
T Consensus 4 d~~~D~vcPwcylg 17 (209)
T cd03021 4 ELYYDVVSPYSYLA 17 (209)
T ss_pred EEEEeCCChHHHHH
Confidence 35568999999973
No 142
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.64 E-value=29 Score=25.32 Aligned_cols=13 Identities=38% Similarity=0.974 Sum_probs=8.3
Q ss_pred CCCcccccccccc
Q 028989 70 EAKNGVCPVCAKR 82 (200)
Q Consensus 70 e~k~vVCPICa~~ 82 (200)
+.++++||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 4566677777654
No 143
>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=27.58 E-value=25 Score=23.87 Aligned_cols=14 Identities=36% Similarity=1.042 Sum_probs=9.0
Q ss_pred CCccceecCCCCcc
Q 028989 39 DDLNAMFLCPFCAE 52 (200)
Q Consensus 39 ~d~r~~F~CPfC~e 52 (200)
+++..+|.||-|+.
T Consensus 29 ~~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 29 EDLPDDWVCPVCGA 42 (47)
T ss_dssp GGS-TT-B-TTTSS
T ss_pred HHCCCCCcCcCCCC
Confidence 36788999999986
No 144
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=27.37 E-value=17 Score=31.39 Aligned_cols=30 Identities=23% Similarity=0.591 Sum_probs=20.2
Q ss_pred eecCCCCccccc--HHHHHhhhhhcCCCC-CCccc
Q 028989 44 MFLCPFCAEDFD--IVGLCCHIDEDHPIE-AKNGV 75 (200)
Q Consensus 44 ~F~CPfC~e~fD--~~~Lc~H~~~eH~~e-~k~vV 75 (200)
.|.||.|...+. ..+| +|..-|.+| +|.|.
T Consensus 2 ~~~CP~C~~~l~~~~~~~--~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSW--ICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEE--EcCCCCCCccccCce
Confidence 389999999653 4445 567788884 45553
No 145
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=26.99 E-value=28 Score=35.76 Aligned_cols=41 Identities=27% Similarity=0.520 Sum_probs=28.8
Q ss_pred CccceecCCCCcccc----cHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 40 DLNAMFLCPFCAEDF----DIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 40 d~r~~F~CPfC~e~f----D~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
+....+.||.|+..+ +...|.||--..+ +..+-.||-|...
T Consensus 440 ~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 440 DCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred cCCCcccCCCCCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 445568999999842 3345666655544 5677899999987
No 146
>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=26.55 E-value=19 Score=28.96 Aligned_cols=23 Identities=13% Similarity=0.377 Sum_probs=15.0
Q ss_pred ccceecCCCCccc-ccHHHHHhhh
Q 028989 41 LNAMFLCPFCAED-FDIVGLCCHI 63 (200)
Q Consensus 41 ~r~~F~CPfC~e~-fD~~~Lc~H~ 63 (200)
.-..|.||||+.- -.+..+....
T Consensus 3 ~~~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 3 IWSDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred EEecCcCccHHHHHHHHHHHHHhC
Confidence 3457899999973 4555555443
No 147
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=26.23 E-value=53 Score=25.85 Aligned_cols=34 Identities=26% Similarity=0.689 Sum_probs=24.2
Q ss_pred CccceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccccchh
Q 028989 40 DLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTD 86 (200)
Q Consensus 40 d~r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d 86 (200)
|+-....||-||.- ||+. ..++|||-|..-+...
T Consensus 5 elGtKR~Cp~CG~kFYDLn-------------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDLN-------------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCcccCCCCcchhccCC-------------CCCccCCCCCCccCcc
Confidence 45567789999984 6642 3568899998876555
No 148
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.22 E-value=12 Score=29.04 Aligned_cols=33 Identities=24% Similarity=0.618 Sum_probs=21.7
Q ss_pred CCCccceecCCCCccc-ccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 38 DDDLNAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 38 d~d~r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
+..+++.+.||+|+.. +. +..+.--.|.-|-..
T Consensus 29 e~~~~~~~~Cp~C~~~~Vk------------R~a~GIW~C~kCg~~ 62 (89)
T COG1997 29 EAQQRAKHVCPFCGRTTVK------------RIATGIWKCRKCGAK 62 (89)
T ss_pred HHHHhcCCcCCCCCCccee------------eeccCeEEcCCCCCe
Confidence 4567889999999875 21 122334468888765
No 149
>PF14828 Amnionless: Amnionless
Probab=26.05 E-value=38 Score=32.52 Aligned_cols=42 Identities=24% Similarity=0.573 Sum_probs=26.5
Q ss_pred cCCCCcccccHHHHHhhh----hhcCCCCCCc---ccccccccccchhhh
Q 028989 46 LCPFCAEDFDIVGLCCHI----DEDHPIEAKN---GVCPVCAKRVGTDIV 88 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~----~~eH~~e~k~---vVCPICa~~v~~d~v 88 (200)
-|+ |+.+.-+..+|..+ ..-||..+-. --||||-++++....
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 455 67766667777655 4455554432 249999999764433
No 150
>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=25.63 E-value=19 Score=24.34 Aligned_cols=11 Identities=36% Similarity=0.639 Sum_probs=8.7
Q ss_pred ceecCCCCccc
Q 028989 43 AMFLCPFCAED 53 (200)
Q Consensus 43 ~~F~CPfC~e~ 53 (200)
..+.||+|..-
T Consensus 5 ~d~~Cp~C~~~ 15 (98)
T cd02972 5 FDPLCPYCYLF 15 (98)
T ss_pred ECCCCHhHHhh
Confidence 35789999884
No 151
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=25.58 E-value=41 Score=29.08 Aligned_cols=11 Identities=27% Similarity=0.948 Sum_probs=8.6
Q ss_pred Ccccccccccc
Q 028989 72 KNGVCPVCAKR 82 (200)
Q Consensus 72 k~vVCPICa~~ 82 (200)
.-.+||.|.+.
T Consensus 34 ~v~~C~~Cg~~ 44 (236)
T PF04981_consen 34 EVTICPKCGRY 44 (236)
T ss_pred CceECCCCCCE
Confidence 44689999885
No 152
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=25.39 E-value=26 Score=26.38 Aligned_cols=17 Identities=29% Similarity=0.722 Sum_probs=10.3
Q ss_pred CCccceecCCCCccccc
Q 028989 39 DDLNAMFLCPFCAEDFD 55 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~fD 55 (200)
-|+-+.|.||-|++..+
T Consensus 60 VENMs~~~Cp~Cg~~~~ 76 (81)
T PF10609_consen 60 VENMSYFVCPHCGERIY 76 (81)
T ss_dssp EECT-EEE-TTT--EEE
T ss_pred EECCCccCCCCCCCeec
Confidence 47788999999998654
No 153
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=25.20 E-value=64 Score=31.22 Aligned_cols=55 Identities=20% Similarity=0.367 Sum_probs=37.3
Q ss_pred eecCCC--Cccc-ccHHHHHhhhhhcC-CCCCCcccccccccc--cchhhhhhhhhhccch
Q 028989 44 MFLCPF--CAED-FDIVGLCCHIDEDH-PIEAKNGVCPVCAKR--VGTDIVSHITMQHGNF 98 (200)
Q Consensus 44 ~F~CPf--C~e~-fD~~~Lc~H~~~eH-~~e~k~vVCPICa~~--v~~d~v~Hlt~qH~~~ 98 (200)
-|.|-+ |-+. =....+..|..+.| -+.+-...|-+|..- -|.++-.||+-+||--
T Consensus 319 ~y~C~h~~C~~s~r~~~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~ 379 (467)
T KOG3608|consen 319 VYQCEHPDCHYSVRTYTQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFR 379 (467)
T ss_pred ceecCCCCCcHHHHHHHHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhccc
Confidence 466666 6654 33455667777777 444455678888775 5679999999988853
No 154
>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=24.88 E-value=18 Score=28.65 Aligned_cols=13 Identities=15% Similarity=0.202 Sum_probs=10.2
Q ss_pred ccceecCCCCccc
Q 028989 41 LNAMFLCPFCAED 53 (200)
Q Consensus 41 ~r~~F~CPfC~e~ 53 (200)
....|.||||+.-
T Consensus 3 ~~~D~~cP~cy~~ 15 (192)
T cd03022 3 FYFDFSSPYSYLA 15 (192)
T ss_pred EEEeCCChHHHHH
Confidence 4457899999984
No 155
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=24.64 E-value=43 Score=23.05 Aligned_cols=33 Identities=24% Similarity=0.555 Sum_probs=12.3
Q ss_pred cceecCCCCcccccHHHHHhhhhhcCCCCCCccccccccc
Q 028989 42 NAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (200)
Q Consensus 42 r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~ 81 (200)
..-++|| |+..+=.- ...++.+ ..+++||-|..
T Consensus 13 ~~~~PC~-Cgf~IC~~-C~~~i~~-----~~~g~CPgCr~ 45 (48)
T PF14570_consen 13 KDFYPCE-CGFQICRF-CYHDILE-----NEGGRCPGCRE 45 (48)
T ss_dssp TT--SST-TS----HH-HHHHHTT-----SS-SB-TTT--
T ss_pred CccccCc-CCCcHHHH-HHHHHHh-----ccCCCCCCCCC
Confidence 3567887 76543211 1122232 34789999965
No 156
>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=24.60 E-value=26 Score=27.33 Aligned_cols=11 Identities=27% Similarity=0.658 Sum_probs=9.2
Q ss_pred ceecCCCCccc
Q 028989 43 AMFLCPFCAED 53 (200)
Q Consensus 43 ~~F~CPfC~e~ 53 (200)
..|.||+|..-
T Consensus 23 ~D~~Cp~C~~~ 33 (178)
T cd03019 23 FSYGCPHCYNF 33 (178)
T ss_pred ECCCCcchhhh
Confidence 46999999884
No 157
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.98 E-value=31 Score=27.15 Aligned_cols=31 Identities=29% Similarity=0.598 Sum_probs=21.8
Q ss_pred CccceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
+.+..+.|+-|+..+..... ....||-|...
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 45789999999976655422 22359999875
No 158
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=23.94 E-value=23 Score=34.63 Aligned_cols=34 Identities=29% Similarity=0.640 Sum_probs=30.2
Q ss_pred cceecCCCCccc-ccHHHHHhhhhhcCCCCCCccc
Q 028989 42 NAMFLCPFCAED-FDIVGLCCHIDEDHPIEAKNGV 75 (200)
Q Consensus 42 r~~F~CPfC~e~-fD~~~Lc~H~~~eH~~e~k~vV 75 (200)
.+-|+|-||-.. +...+|-.||+.-|+.|.++|.
T Consensus 456 ~q~f~~ky~~atfyss~~ltrhin~~Hpse~rqv~ 490 (500)
T KOG3993|consen 456 EQGFTCKYCPATFYSSPGLTRHINKCHPSELRQVA 490 (500)
T ss_pred hhccccccchHhhhcCcchHhHhhhcChHHhhhhH
Confidence 467999999986 8899999999999999999874
No 159
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.94 E-value=44 Score=31.52 Aligned_cols=24 Identities=25% Similarity=0.559 Sum_probs=20.0
Q ss_pred CCccceecCCCCcccccHHHHHhh
Q 028989 39 DDLNAMFLCPFCAEDFDIVGLCCH 62 (200)
Q Consensus 39 ~d~r~~F~CPfC~e~fD~~~Lc~H 62 (200)
+-+...|+||.|+..|-..+|..|
T Consensus 15 ~q~~~~fpc~ic~r~f~~~~L~kh 38 (351)
T KOG3940|consen 15 AQMQMRFPCRICQREFRRRELMKH 38 (351)
T ss_pred ccccccccccccccchhhhhhhcc
Confidence 456679999999988888888776
No 160
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=23.76 E-value=36 Score=29.17 Aligned_cols=14 Identities=43% Similarity=0.921 Sum_probs=11.1
Q ss_pred ecCCCCcccccHHH
Q 028989 45 FLCPFCAEDFDIVG 58 (200)
Q Consensus 45 F~CPfC~e~fD~~~ 58 (200)
=+||+|+.-+|-.+
T Consensus 155 P~CPlCg~PlDP~G 168 (171)
T PF11290_consen 155 PPCPLCGEPLDPEG 168 (171)
T ss_pred CCCCCCCCCCCCCC
Confidence 47999999887543
No 161
>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=23.57 E-value=44 Score=32.18 Aligned_cols=33 Identities=33% Similarity=0.886 Sum_probs=16.4
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCccccccccc-ccchhhh
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK-RVGTDIV 88 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~-~v~~d~v 88 (200)
+.-.||||+..+.. +-+.-+||||-. .||.+-+
T Consensus 379 ~~v~CP~cgA~y~~-------------~~kG~lC~vC~l~~IG~~a~ 412 (422)
T PF06957_consen 379 PSVKCPYCGAKYHP-------------EYKGQLCPVCELSEIGADAS 412 (422)
T ss_dssp -EEE-TTT--EEEG-------------GGTTSB-TTTTTBBTT---S
T ss_pred CCeeCCCCCCccCh-------------hhCCCCCCCCcceeeCCcce
Confidence 45779999876532 234569999976 4776554
No 162
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=23.38 E-value=39 Score=23.39 Aligned_cols=22 Identities=32% Similarity=0.730 Sum_probs=19.2
Q ss_pred CCCcccccccccccchhhhhhhh
Q 028989 70 EAKNGVCPVCAKRVGTDIVSHIT 92 (200)
Q Consensus 70 e~k~vVCPICa~~v~~d~v~Hlt 92 (200)
+.|.|.|-+|..+.. ||..||.
T Consensus 2 ~~k~GYCE~Cr~kfd-~l~~Hi~ 23 (49)
T smart00586 2 EKKPGYCENCREKYD-DLETHLL 23 (49)
T ss_pred CCCCcccccHhHHHh-hHHHHhc
Confidence 678999999999876 9999984
No 163
>PHA02929 N1R/p28-like protein; Provisional
Probab=23.31 E-value=13 Score=33.13 Aligned_cols=43 Identities=23% Similarity=0.377 Sum_probs=24.4
Q ss_pred cceecCCCCcccccHH----------HHHhhhhhcCCC---CCCcccccccccccc
Q 028989 42 NAMFLCPFCAEDFDIV----------GLCCHIDEDHPI---EAKNGVCPVCAKRVG 84 (200)
Q Consensus 42 r~~F~CPfC~e~fD~~----------~Lc~H~~~eH~~---e~k~vVCPICa~~v~ 84 (200)
..+..||.|.+.+... .=|.|+--..|. -.....||+|...+.
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 3456999999974321 125553222222 123468999988654
No 164
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.28 E-value=16 Score=25.10 Aligned_cols=30 Identities=20% Similarity=0.641 Sum_probs=16.9
Q ss_pred cCCCCcccccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 46 LCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 46 ~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
.|+.|+.++-.-.- -.+.+ . .||.-|..++
T Consensus 1 ~C~iCg~kigl~~~-~k~~D-----G--~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR-FKIKD-----G--YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc-eeccC-----c--cchHHHHHHh
Confidence 48888876443221 11211 1 4888888776
No 165
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=23.20 E-value=30 Score=32.17 Aligned_cols=18 Identities=28% Similarity=0.617 Sum_probs=14.3
Q ss_pred Ccccccccccccchhhhh
Q 028989 72 KNGVCPVCAKRVGTDIVS 89 (200)
Q Consensus 72 k~vVCPICa~~v~~d~v~ 89 (200)
+..+||||..++...||.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 346999999998777763
No 166
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.03 E-value=26 Score=26.75 Aligned_cols=37 Identities=22% Similarity=0.534 Sum_probs=27.0
Q ss_pred ceecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccccchhh
Q 028989 43 AMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRVGTDI 87 (200)
Q Consensus 43 ~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v~~d~ 87 (200)
..|.|--|+..+|++ .|+.+ .-...||-|.+++.+-|
T Consensus 11 Y~Y~c~~cg~~~dvv---q~~~d-----dplt~ce~c~a~~kk~l 47 (82)
T COG2331 11 YSYECTECGNRFDVV---QAMTD-----DPLTTCEECGARLKKLL 47 (82)
T ss_pred eEEeecccchHHHHH---Hhccc-----CccccChhhChHHHHhh
Confidence 478999999988865 34443 44578999999766544
No 167
>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=22.82 E-value=28 Score=26.54 Aligned_cols=8 Identities=38% Similarity=1.215 Sum_probs=6.1
Q ss_pred ecCCCCcc
Q 028989 45 FLCPFCAE 52 (200)
Q Consensus 45 F~CPfC~e 52 (200)
.+||+|++
T Consensus 2 I~CP~CG~ 9 (84)
T PF04267_consen 2 IPCPHCGP 9 (84)
T ss_dssp EEETTTEE
T ss_pred ccCCCCCc
Confidence 36888887
No 168
>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=22.60 E-value=16 Score=27.93 Aligned_cols=22 Identities=27% Similarity=0.377 Sum_probs=15.8
Q ss_pred cceecCCCCccc-ccHHHHHhhh
Q 028989 42 NAMFLCPFCAED-FDIVGLCCHI 63 (200)
Q Consensus 42 r~~F~CPfC~e~-fD~~~Lc~H~ 63 (200)
-..|.||+|... -.+..|..+.
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 457999999984 5666777775
No 169
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=22.54 E-value=62 Score=21.74 Aligned_cols=32 Identities=19% Similarity=0.572 Sum_probs=20.3
Q ss_pred CccceecCCCCcccccHHHHHhhhhhcCCCCCCccccccc
Q 028989 40 DLNAMFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVC 79 (200)
Q Consensus 40 d~r~~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPIC 79 (200)
.....+.||.|+-++....= .+. .+..-||.|
T Consensus 24 ~~~v~W~C~~Cgh~w~~~v~-------~R~-~~~~~CP~C 55 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWKASVN-------DRT-RRGKGCPYC 55 (55)
T ss_pred CCEEEEECCCCCCeeEccHh-------hhc-cCCCCCCCC
Confidence 45667999999876543221 111 455789988
No 170
>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=22.53 E-value=52 Score=24.87 Aligned_cols=31 Identities=23% Similarity=0.376 Sum_probs=25.1
Q ss_pred CCCCcccccccccccc-hhhhhhhhhhccchh
Q 028989 69 IEAKNGVCPVCAKRVG-TDIVSHITMQHGNFF 99 (200)
Q Consensus 69 ~e~k~vVCPICa~~v~-~d~v~Hlt~qH~~~~ 99 (200)
.+.+.+||-.|...|. ..+.+||+..|....
T Consensus 7 ~~~~vlIC~~C~~av~~~~v~~HL~~~H~~~~ 38 (109)
T PF12013_consen 7 PEYRVLICRQCQYAVQPSEVESHLRKRHHILK 38 (109)
T ss_pred CcCCEEEeCCCCcccCchHHHHHHHHhccccc
Confidence 4567789999998866 799999988777763
No 171
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=22.28 E-value=33 Score=36.09 Aligned_cols=47 Identities=26% Similarity=0.518 Sum_probs=37.5
Q ss_pred eecCCCCcccc-cHHHHHhhhhhcCCCCCCcccccccccccc--hhhhhhhh
Q 028989 44 MFLCPFCAEDF-DIVGLCCHIDEDHPIEAKNGVCPVCAKRVG--TDIVSHIT 92 (200)
Q Consensus 44 ~F~CPfC~e~f-D~~~Lc~H~~~eH~~e~k~vVCPICa~~v~--~d~v~Hlt 92 (200)
.-.|-||++-| -...|.-|+..+ .-.++-+|-||..+.+ .|+--|+.
T Consensus 353 khkCr~CakvfgS~SaLqiHlRSH--TGERPfqCnvCG~~FSTkGNLKvH~~ 402 (958)
T KOG1074|consen 353 KHKCRFCAKVFGSDSALQIHLRSH--TGERPFQCNVCGNRFSTKGNLKVHFQ 402 (958)
T ss_pred cchhhhhHhhcCchhhhhhhhhcc--CCCCCeeecccccccccccceeeeee
Confidence 34599999964 567899999876 5567889999999966 48888873
No 172
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=22.27 E-value=59 Score=20.57 Aligned_cols=32 Identities=25% Similarity=0.646 Sum_probs=17.5
Q ss_pred ecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
..||-|+..|.+..= .=+...+.|-||.|...
T Consensus 3 i~CP~C~~~f~v~~~------~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD------KLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHH------HcccCCcEEECCCCCcE
Confidence 468888875444321 01223456778887653
No 173
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.02 E-value=40 Score=36.87 Aligned_cols=36 Identities=28% Similarity=0.513 Sum_probs=17.2
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCccccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKRV 83 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~v 83 (200)
.+.||-|+...- ...|..|-.. .++ ..+||.|-+.+
T Consensus 667 ~rkCPkCG~~t~-~~fCP~CGs~--te~-vy~CPsCGaev 702 (1337)
T PRK14714 667 RRRCPSCGTETY-ENRCPDCGTH--TEP-VYVCPDCGAEV 702 (1337)
T ss_pred EEECCCCCCccc-cccCcccCCc--CCC-ceeCccCCCcc
Confidence 477877777421 1255444433 111 22455555543
No 174
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.99 E-value=27 Score=31.04 Aligned_cols=53 Identities=19% Similarity=0.295 Sum_probs=33.7
Q ss_pred CccceecCCCCcc-cccHHHHHhhhh-------hcCCCCCCcccccccccccchhhhhhhhhhccc
Q 028989 40 DLNAMFLCPFCAE-DFDIVGLCCHID-------EDHPIEAKNGVCPVCAKRVGTDIVSHITMQHGN 97 (200)
Q Consensus 40 d~r~~F~CPfC~e-~fD~~~Lc~H~~-------~eH~~e~k~vVCPICa~~v~~d~v~Hlt~qH~~ 97 (200)
|..+.+.||+|+. .-.+..+..-.. .-||++..+..||- |.|...++...-|.
T Consensus 9 ~v~sD~vCPwC~ig~~rL~ka~~~~~~~~~v~i~w~pf~l~p~~~~~-----g~~~~~~l~~k~g~ 69 (225)
T COG2761 9 DVFSDVVCPWCYIGKRRLEKALAEYPQEVRVEIRWRPFELDPDLPPE-----GLDRKEYLAQKYGI 69 (225)
T ss_pred EEEeCCcCchhhcCHHHHHHHHHhcCcceeEEEEecccccCCCCCcc-----cccHHHHHHHHhCc
Confidence 5677899999987 333333332222 34788888888876 66777776544443
No 175
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.89 E-value=53 Score=30.26 Aligned_cols=29 Identities=21% Similarity=0.241 Sum_probs=21.3
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
--.||-|++.+....|-. +..|||-|...
T Consensus 38 w~kc~~C~~~~~~~~l~~----------~~~vcp~c~~h 66 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKS----------KMNICEQCGYH 66 (296)
T ss_pred eeECCCccchhhHHHHHH----------cCCCCCCCCCC
Confidence 347999999876666532 33699999875
No 176
>PRK05978 hypothetical protein; Provisional
Probab=21.68 E-value=73 Score=26.57 Aligned_cols=27 Identities=26% Similarity=0.597 Sum_probs=18.1
Q ss_pred eecCCCCccc--ccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 44 MFLCPFCAED--FDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 44 ~F~CPfC~e~--fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
.-.||-|++- |+ .+-.-+--||+|...
T Consensus 33 ~grCP~CG~G~LF~------------g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 33 RGRCPACGEGKLFR------------AFLKPVDHCAACGED 61 (148)
T ss_pred cCcCCCCCCCcccc------------cccccCCCccccCCc
Confidence 4689999993 64 222334568888876
No 177
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=21.58 E-value=65 Score=22.41 Aligned_cols=21 Identities=24% Similarity=0.387 Sum_probs=11.8
Q ss_pred cccHHHHHhhhhhcCCCCCCcccccc
Q 028989 53 DFDIVGLCCHIDEDHPIEAKNGVCPV 78 (200)
Q Consensus 53 ~fD~~~Lc~H~~~eH~~e~k~vVCPI 78 (200)
-||...+..++ ...+...||+
T Consensus 33 ~fek~aI~~~i-----~~~~~~~CPv 53 (57)
T PF11789_consen 33 TFEKEAILQYI-----QRNGSKRCPV 53 (57)
T ss_dssp EEEHHHHHHHC-----TTTS-EE-SC
T ss_pred eecHHHHHHHH-----HhcCCCCCCC
Confidence 35666666666 2355678888
No 178
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=21.33 E-value=45 Score=21.82 Aligned_cols=10 Identities=40% Similarity=1.205 Sum_probs=7.8
Q ss_pred ceecCCCCcc
Q 028989 43 AMFLCPFCAE 52 (200)
Q Consensus 43 ~~F~CPfC~e 52 (200)
..|.||.|+-
T Consensus 17 ~g~~CP~Cg~ 26 (46)
T PF12760_consen 17 DGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCC
Confidence 3588999986
No 179
>PHA00733 hypothetical protein
Probab=21.14 E-value=74 Score=25.37 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=21.9
Q ss_pred eecCCCCccc-ccHHHHHhhhhhcCC
Q 028989 44 MFLCPFCAED-FDIVGLCCHIDEDHP 68 (200)
Q Consensus 44 ~F~CPfC~e~-fD~~~Lc~H~~~eH~ 68 (200)
.|.|+.|++. -....|..|+...|.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 5899999997 667889999999986
No 180
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=20.92 E-value=28 Score=26.05 Aligned_cols=11 Identities=18% Similarity=0.609 Sum_probs=9.0
Q ss_pred ceecCCCCccc
Q 028989 43 AMFLCPFCAED 53 (200)
Q Consensus 43 ~~F~CPfC~e~ 53 (200)
..|.||||...
T Consensus 13 ~D~~Cp~C~~~ 23 (154)
T cd03023 13 FDYNCGYCKKL 23 (154)
T ss_pred ECCCChhHHHh
Confidence 46899999874
No 181
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=20.60 E-value=64 Score=20.44 Aligned_cols=31 Identities=23% Similarity=0.642 Sum_probs=16.9
Q ss_pred ecCCCCcccccHHHHHhhhhhcCCCCCCccccccccc
Q 028989 45 FLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAK 81 (200)
Q Consensus 45 F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~ 81 (200)
..||-|...|++..= .=+.....+-||.|..
T Consensus 3 i~Cp~C~~~y~i~d~------~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDE------KIPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHH------HCCCCCcEEECCCCCC
Confidence 467777775544321 1133345566777754
No 182
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.44 E-value=62 Score=29.39 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=21.1
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
--.||-|++.+-...|-. +..|||-|...
T Consensus 26 ~~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELER----------NLEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHh----------hCCCCCCCCCc
Confidence 347999999866665532 23699999885
No 183
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=20.32 E-value=60 Score=29.58 Aligned_cols=29 Identities=28% Similarity=0.573 Sum_probs=21.2
Q ss_pred eecCCCCcccccHHHHHhhhhhcCCCCCCcccccccccc
Q 028989 44 MFLCPFCAEDFDIVGLCCHIDEDHPIEAKNGVCPVCAKR 82 (200)
Q Consensus 44 ~F~CPfC~e~fD~~~Lc~H~~~eH~~e~k~vVCPICa~~ 82 (200)
--.||-|++.+-...|-. +..|||-|...
T Consensus 27 ~~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEA----------NLNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHh----------cCCCCCCCCCC
Confidence 458999999776666532 23599999885
Done!