Query 027681
Match_columns 220
No_of_seqs 127 out of 146
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 13:35:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027681.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027681hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05605 zf-Di19: Drought indu 99.8 1.8E-19 3.8E-24 125.2 3.5 53 44-96 2-54 (54)
2 PF14571 Di19_C: Stress-induce 99.5 8E-15 1.7E-19 115.6 2.0 76 115-192 2-82 (105)
3 KOG1280 Uncharacterized conser 97.6 3.8E-05 8.2E-10 72.3 3.0 41 43-83 78-119 (381)
4 KOG2923 Uncharacterized conser 94.7 0.011 2.4E-07 44.0 0.6 45 30-83 7-54 (67)
5 COG5216 Uncharacterized conser 94.3 0.021 4.7E-07 42.2 1.4 36 39-83 17-54 (67)
6 PF13894 zf-C2H2_4: C2H2-type 89.9 0.18 3.9E-06 27.8 1.2 23 45-67 1-24 (24)
7 PHA00732 hypothetical protein 89.4 0.33 7.1E-06 36.7 2.6 42 45-91 2-44 (79)
8 PF13913 zf-C2HC_2: zinc-finge 88.8 0.27 5.8E-06 29.6 1.4 21 44-64 2-22 (25)
9 smart00531 TFIIE Transcription 88.2 0.39 8.4E-06 39.4 2.5 40 39-83 94-133 (147)
10 PF13909 zf-H2C2_5: C2H2-type 88.1 0.25 5.5E-06 28.5 1.0 24 45-68 1-24 (24)
11 KOG1842 FYVE finger-containing 87.1 0.24 5.1E-06 48.7 0.7 35 39-73 10-45 (505)
12 PLN03086 PRLI-interacting fact 86.4 0.62 1.4E-05 46.7 3.2 45 44-93 453-498 (567)
13 PF09237 GAGA: GAGA factor; I 85.9 0.49 1.1E-05 34.1 1.6 27 71-97 22-50 (54)
14 smart00834 CxxC_CXXC_SSSS Puta 84.0 0.44 9.5E-06 30.4 0.6 33 43-83 4-36 (41)
15 PF12756 zf-C2H2_2: C2H2 type 83.8 0.6 1.3E-05 33.7 1.4 48 46-93 1-72 (100)
16 PF00096 zf-C2H2: Zinc finger, 83.0 0.56 1.2E-05 26.5 0.7 21 45-65 1-22 (23)
17 TIGR01206 lysW lysine biosynth 82.5 0.43 9.3E-06 34.1 0.2 30 44-82 2-31 (54)
18 PF08271 TF_Zn_Ribbon: TFIIB z 82.2 0.59 1.3E-05 30.9 0.7 35 45-89 1-35 (43)
19 PF14354 Lar_restr_allev: Rest 81.8 0.46 1E-05 33.0 0.1 31 44-81 3-37 (61)
20 PF09986 DUF2225: Uncharacteri 81.2 0.5 1.1E-05 41.2 0.1 49 44-92 5-67 (214)
21 PF04780 DUF629: Protein of un 81.2 0.95 2.1E-05 44.5 2.0 50 42-91 55-105 (466)
22 PF08274 PhnA_Zn_Ribbon: PhnA 81.0 0.57 1.2E-05 29.9 0.3 24 46-81 4-27 (30)
23 PRK09710 lar restriction allev 81.0 0.62 1.3E-05 34.6 0.5 32 44-84 6-38 (64)
24 TIGR02605 CxxC_CxxC_SSSS putat 80.3 0.75 1.6E-05 31.1 0.7 32 43-82 4-35 (52)
25 PLN03208 E3 ubiquitin-protein 80.1 0.8 1.7E-05 40.3 1.0 50 42-91 16-86 (193)
26 TIGR02098 MJ0042_CXXC MJ0042 f 80.0 0.9 1.9E-05 29.0 1.0 32 45-82 3-34 (38)
27 COG5236 Uncharacterized conser 79.7 2.2 4.8E-05 41.4 3.9 36 41-82 217-253 (493)
28 smart00504 Ubox Modified RING 79.1 1.9 4.1E-05 29.4 2.4 29 50-85 19-47 (63)
29 PF07191 zinc-ribbons_6: zinc- 75.5 0.31 6.7E-06 36.7 -2.5 56 45-104 2-64 (70)
30 PHA00733 hypothetical protein 74.8 3.9 8.6E-05 33.2 3.6 48 44-95 73-123 (128)
31 PF12756 zf-C2H2_2: C2H2 type 71.9 2.3 5E-05 30.6 1.4 25 43-67 49-74 (100)
32 PF14255 Cys_rich_CPXG: Cystei 71.7 1.4 3E-05 31.2 0.2 34 45-83 1-34 (52)
33 PRK00398 rpoP DNA-directed RNA 70.4 2.8 6E-05 28.0 1.5 29 44-83 3-31 (46)
34 cd00350 rubredoxin_like Rubred 70.4 2.2 4.8E-05 27.0 0.9 25 45-82 2-26 (33)
35 PLN03086 PRLI-interacting fact 69.3 4.2 9.2E-05 41.0 3.1 38 43-83 477-514 (567)
36 PF03145 Sina: Seven in absent 69.3 3.1 6.7E-05 35.2 1.8 54 43-99 13-75 (198)
37 PF08996 zf-DNA_Pol: DNA Polym 69.1 1.5 3.3E-05 37.4 -0.1 53 42-96 16-69 (188)
38 COG5175 MOT2 Transcriptional r 68.6 1.2 2.6E-05 43.0 -0.8 36 47-83 17-63 (480)
39 PRK14892 putative transcriptio 68.6 2.1 4.5E-05 34.0 0.6 38 41-86 18-55 (99)
40 KOG2462 C2H2-type Zn-finger pr 67.4 4.4 9.5E-05 37.7 2.5 37 42-82 159-196 (279)
41 TIGR00373 conserved hypothetic 67.2 4.3 9.3E-05 34.0 2.2 35 39-83 104-138 (158)
42 PF03470 zf-XS: XS zinc finger 66.9 3.4 7.4E-05 28.5 1.3 16 47-62 1-20 (43)
43 PF09723 Zn-ribbon_8: Zinc rib 66.9 1.8 3.9E-05 28.8 -0.0 31 43-81 4-34 (42)
44 PRK06266 transcription initiat 66.8 4.8 0.0001 34.4 2.5 35 39-83 112-146 (178)
45 smart00734 ZnF_Rad18 Rad18-lik 65.5 4.3 9.4E-05 24.7 1.5 19 46-64 3-21 (26)
46 cd00729 rubredoxin_SM Rubredox 64.3 3.7 8E-05 26.4 1.0 26 44-82 2-27 (34)
47 PF02176 zf-TRAF: TRAF-type zi 64.0 3.3 7.1E-05 28.2 0.8 45 44-90 9-60 (60)
48 PF05129 Elf1: Transcription e 62.0 3.2 6.9E-05 31.5 0.5 35 41-82 19-55 (81)
49 KOG0320 Predicted E3 ubiquitin 61.7 4.4 9.5E-05 35.7 1.3 44 42-85 129-179 (187)
50 PHA02768 hypothetical protein; 60.3 6.9 0.00015 28.2 1.9 34 44-81 5-39 (55)
51 COG1655 Uncharacterized protei 59.8 3.6 7.8E-05 37.8 0.5 13 43-55 18-30 (267)
52 TIGR03655 anti_R_Lar restricti 59.7 3.9 8.6E-05 28.2 0.6 9 75-83 28-36 (53)
53 PRK12496 hypothetical protein; 59.4 3.7 8E-05 34.7 0.5 29 43-84 126-154 (164)
54 PF13465 zf-H2C2_2: Zinc-finge 58.9 3.5 7.6E-05 24.6 0.2 11 44-54 14-24 (26)
55 PTZ00255 60S ribosomal protein 58.8 2.5 5.4E-05 33.3 -0.6 16 37-52 29-44 (90)
56 PF12773 DZR: Double zinc ribb 58.7 5.2 0.00011 26.6 1.1 28 46-85 14-41 (50)
57 PF14206 Cys_rich_CPCC: Cystei 56.0 6.8 0.00015 29.9 1.4 26 45-81 2-28 (78)
58 PF07754 DUF1610: Domain of un 53.1 8 0.00017 23.7 1.1 12 41-52 13-24 (24)
59 PF08209 Sgf11: Sgf11 (transcr 53.0 8.2 0.00018 25.1 1.2 22 43-64 3-24 (33)
60 PF04423 Rad50_zn_hook: Rad50 52.9 6.9 0.00015 26.9 0.9 11 75-85 22-32 (54)
61 TIGR00280 L37a ribosomal prote 52.5 3.5 7.7E-05 32.5 -0.7 16 37-52 28-43 (91)
62 TIGR00100 hypA hydrogenase nic 51.9 6.2 0.00013 31.4 0.6 31 39-82 65-95 (115)
63 PRK03976 rpl37ae 50S ribosomal 51.6 3.8 8.2E-05 32.2 -0.6 16 37-52 29-44 (90)
64 KOG3623 Homeobox transcription 51.4 6.4 0.00014 41.4 0.8 41 42-82 208-249 (1007)
65 PRK14890 putative Zn-ribbon RN 51.2 11 0.00025 27.6 1.8 34 40-80 21-55 (59)
66 PF04564 U-box: U-box domain; 51.1 21 0.00046 25.8 3.3 37 43-85 3-51 (73)
67 PF13395 HNH_4: HNH endonuclea 50.5 8 0.00017 26.7 0.9 14 47-60 1-14 (54)
68 TIGR00686 phnA alkylphosphonat 50.0 6.9 0.00015 31.9 0.6 12 71-82 17-28 (109)
69 KOG1002 Nucleotide excision re 49.3 9.4 0.0002 39.0 1.6 54 37-91 529-593 (791)
70 KOG2593 Transcription initiati 48.8 6.9 0.00015 38.4 0.5 43 33-82 117-162 (436)
71 PF02892 zf-BED: BED zinc fing 48.4 8.7 0.00019 24.9 0.8 26 42-67 14-44 (45)
72 smart00659 RPOLCX RNA polymera 47.8 11 0.00024 25.6 1.3 28 44-83 2-29 (44)
73 PRK12495 hypothetical protein; 47.6 9.8 0.00021 34.5 1.3 30 43-85 41-70 (226)
74 smart00507 HNHc HNH nucleases. 47.4 4.5 9.8E-05 25.5 -0.7 21 45-65 11-31 (52)
75 PF01155 HypA: Hydrogenase exp 47.1 7.1 0.00015 30.9 0.3 31 39-82 65-95 (113)
76 COG4311 SoxD Sarcosine oxidase 47.1 8.6 0.00019 30.8 0.7 9 44-52 3-11 (97)
77 PF02146 SIR2: Sir2 family; I 46.7 12 0.00027 30.9 1.6 40 43-87 104-143 (178)
78 PF07282 OrfB_Zn_ribbon: Putat 46.4 16 0.00034 25.8 1.9 41 40-91 24-64 (69)
79 PRK12380 hydrogenase nickel in 44.7 9.3 0.0002 30.4 0.6 31 39-82 65-95 (113)
80 PF05876 Terminase_GpA: Phage 44.6 13 0.00027 37.0 1.6 42 42-85 198-241 (557)
81 PF13248 zf-ribbon_3: zinc-rib 44.3 14 0.0003 22.2 1.2 10 45-54 3-12 (26)
82 smart00614 ZnF_BED BED zinc fi 44.3 15 0.00032 24.9 1.4 26 43-68 17-48 (50)
83 PRK03824 hypA hydrogenase nick 44.2 13 0.00027 30.5 1.3 43 40-82 66-116 (135)
84 PF05207 zf-CSL: CSL zinc fing 43.0 14 0.00029 26.1 1.2 44 32-84 5-51 (55)
85 PF10571 UPF0547: Uncharacteri 43.0 14 0.00031 22.6 1.1 8 47-54 3-10 (26)
86 COG4888 Uncharacterized Zn rib 42.9 12 0.00025 30.4 0.9 37 41-82 19-55 (104)
87 COG1592 Rubrerythrin [Energy p 41.9 17 0.00038 31.3 1.9 25 44-82 134-158 (166)
88 PRK00464 nrdR transcriptional 41.8 16 0.00034 31.0 1.6 31 46-82 2-37 (154)
89 PF01844 HNH: HNH endonuclease 41.5 5.2 0.00011 25.7 -1.1 35 47-81 1-42 (47)
90 COG4049 Uncharacterized protei 41.5 9.7 0.00021 28.2 0.2 24 76-99 20-45 (65)
91 PF13240 zinc_ribbon_2: zinc-r 41.5 9.6 0.00021 22.6 0.2 7 47-53 2-8 (23)
92 PF00301 Rubredoxin: Rubredoxi 41.4 11 0.00024 26.1 0.5 14 39-52 29-42 (47)
93 PF01780 Ribosomal_L37ae: Ribo 40.4 5.4 0.00012 31.4 -1.3 15 38-52 29-43 (90)
94 COG2888 Predicted Zn-ribbon RN 40.2 26 0.00057 25.9 2.3 35 39-80 22-57 (61)
95 PF15616 TerY-C: TerY-C metal 39.5 10 0.00022 31.6 0.1 42 44-87 77-119 (131)
96 smart00355 ZnF_C2H2 zinc finge 39.4 24 0.00051 19.0 1.6 20 45-64 1-21 (26)
97 PRK11595 DNA utilization prote 39.3 15 0.00033 31.8 1.2 35 46-82 7-43 (227)
98 PRK03922 hypothetical protein; 39.2 13 0.00029 30.4 0.7 15 44-58 49-63 (113)
99 PRK00420 hypothetical protein; 39.1 20 0.00043 29.1 1.7 27 45-83 24-50 (112)
100 PF13912 zf-C2H2_6: C2H2-type 38.8 20 0.00043 20.7 1.3 22 45-66 2-24 (27)
101 PF04475 DUF555: Protein of un 38.6 14 0.0003 29.9 0.7 15 44-58 47-61 (102)
102 cd00730 rubredoxin Rubredoxin; 38.2 19 0.0004 25.2 1.2 14 39-52 29-42 (50)
103 COG0675 Transposase and inacti 38.1 21 0.00045 30.7 1.8 37 39-91 304-340 (364)
104 PHA02929 N1R/p28-like protein; 37.7 6.8 0.00015 35.4 -1.3 44 41-84 171-227 (238)
105 PF06957 COPI_C: Coatomer (COP 37.6 17 0.00036 35.5 1.2 34 43-89 379-413 (422)
106 PRK11088 rrmA 23S rRNA methylt 36.6 12 0.00026 32.8 0.1 32 44-75 2-34 (272)
107 PF11672 DUF3268: Protein of u 36.3 17 0.00037 29.1 0.9 38 45-85 3-43 (102)
108 KOG2817 Predicted E3 ubiquitin 35.5 19 0.00042 35.0 1.3 15 44-58 374-388 (394)
109 PF14570 zf-RING_4: RING/Ubox 35.4 13 0.00028 26.1 0.1 33 42-81 13-45 (48)
110 KOG2231 Predicted E3 ubiquitin 35.4 23 0.00051 36.6 1.9 30 41-70 179-209 (669)
111 PF14634 zf-RING_5: zinc-RING 35.3 24 0.00052 23.0 1.4 10 71-80 34-43 (44)
112 PHA00616 hypothetical protein 34.4 21 0.00046 24.6 1.0 23 45-67 2-25 (44)
113 cd03021 DsbA_GSTK DsbA family, 34.3 9.2 0.0002 32.2 -1.0 14 40-53 4-17 (209)
114 COG1499 NMD3 NMD protein affec 34.0 22 0.00048 33.9 1.4 41 42-82 4-52 (355)
115 PF11789 zf-Nse: Zinc-finger o 34.0 35 0.00075 24.2 2.1 33 41-78 8-53 (57)
116 COG5109 Uncharacterized conser 33.7 19 0.00041 34.7 0.9 10 43-52 375-384 (396)
117 TIGR00570 cdk7 CDK-activating 33.7 20 0.00043 33.8 1.0 38 45-83 4-53 (309)
118 cd03024 DsbA_FrnE DsbA family, 33.2 12 0.00026 30.5 -0.5 34 183-218 156-190 (201)
119 PF12660 zf-TFIIIC: Putative z 32.5 11 0.00024 29.4 -0.7 38 46-83 16-65 (99)
120 cd03022 DsbA_HCCA_Iso DsbA fam 30.9 12 0.00025 30.1 -0.8 36 180-217 145-180 (192)
121 PRK04023 DNA polymerase II lar 30.6 27 0.00058 38.0 1.4 38 43-84 637-674 (1121)
122 COG5189 SFP1 Putative transcri 30.5 25 0.00054 34.0 1.1 41 43-83 348-408 (423)
123 KOG2177 Predicted E3 ubiquitin 30.1 7.9 0.00017 31.4 -2.0 40 41-80 10-54 (386)
124 PF11793 FANCL_C: FANCL C-term 30.0 29 0.00063 25.3 1.2 47 39-85 15-67 (70)
125 PF04780 DUF629: Protein of un 29.8 26 0.00056 34.8 1.1 29 72-100 56-86 (466)
126 PF03966 Trm112p: Trm112p-like 29.6 38 0.00083 24.2 1.7 37 44-81 7-61 (68)
127 PF13824 zf-Mss51: Zinc-finger 29.4 16 0.00036 26.3 -0.2 10 42-51 12-21 (55)
128 PRK12860 transcriptional activ 29.1 42 0.0009 29.6 2.2 32 39-80 129-161 (189)
129 KOG2462 C2H2-type Zn-finger pr 29.1 36 0.00077 31.8 1.8 52 44-97 187-241 (279)
130 PF10609 ParA: ParA/MinD ATPas 27.1 24 0.00051 27.1 0.3 18 39-56 60-77 (81)
131 PF14968 CCDC84: Coiled coil p 26.9 32 0.0007 32.7 1.2 20 38-57 52-71 (336)
132 KOG4696 Uncharacterized conser 26.5 33 0.0007 33.0 1.2 22 44-65 2-23 (393)
133 PF14311 DUF4379: Domain of un 26.5 49 0.0011 22.6 1.8 39 33-79 17-55 (55)
134 cd02972 DsbA_family DsbA famil 26.5 17 0.00038 24.9 -0.5 10 43-52 5-14 (98)
135 PRK05477 gatB aspartyl/glutamy 26.4 32 0.0007 34.0 1.2 19 67-85 31-49 (474)
136 KOG2879 Predicted E3 ubiquitin 26.1 22 0.00047 33.5 -0.1 40 44-83 239-286 (298)
137 COG1675 TFA1 Transcription ini 26.1 49 0.0011 28.8 2.1 31 41-83 110-142 (176)
138 PF10058 DUF2296: Predicted in 25.8 34 0.00073 24.2 0.9 9 44-52 44-52 (54)
139 PRK05654 acetyl-CoA carboxylas 25.5 44 0.00096 30.9 1.8 29 44-82 27-55 (292)
140 PF04267 SoxD: Sarcosine oxida 25.3 24 0.00053 27.4 0.1 8 45-52 2-9 (84)
141 PF09538 FYDLN_acid: Protein o 24.8 34 0.00074 27.4 0.8 34 40-86 5-39 (108)
142 COG1997 RPL43A Ribosomal prote 24.8 18 0.00038 28.6 -0.8 18 36-53 27-44 (89)
143 TIGR00515 accD acetyl-CoA carb 24.8 48 0.001 30.6 1.9 29 44-82 26-54 (285)
144 PRK00564 hypA hydrogenase nick 24.6 33 0.00071 27.4 0.7 32 39-82 66-97 (117)
145 PF13462 Thioredoxin_4: Thiore 24.3 13 0.00028 28.8 -1.6 21 43-63 20-41 (162)
146 PF14353 CpXC: CpXC protein 24.2 38 0.00082 26.7 1.0 15 43-57 37-51 (128)
147 PF09334 tRNA-synt_1g: tRNA sy 24.2 25 0.00054 33.3 -0.1 40 44-83 136-176 (391)
148 PF11290 DUF3090: Protein of u 24.1 35 0.00075 29.8 0.8 14 45-58 155-168 (171)
149 TIGR00599 rad18 DNA repair pro 24.1 21 0.00045 34.6 -0.6 47 39-85 21-72 (397)
150 COG2761 FrnE Predicted dithiol 24.1 23 0.00051 31.9 -0.2 47 170-218 152-199 (225)
151 KOG4173 Alpha-SNAP protein [In 24.0 34 0.00074 31.2 0.8 54 43-100 78-135 (253)
152 CHL00174 accD acetyl-CoA carbo 23.7 50 0.0011 30.9 1.8 29 44-82 38-66 (296)
153 PF14616 DUF4451: Domain of un 23.6 47 0.001 26.9 1.4 24 73-96 25-53 (124)
154 PF00097 zf-C3HC4: Zinc finger 23.1 11 0.00025 23.7 -1.8 8 72-79 34-41 (41)
155 PF14828 Amnionless: Amnionles 22.9 54 0.0012 32.0 1.9 42 45-87 192-240 (437)
156 cd03019 DsbA_DsbA DsbA family, 22.9 31 0.00066 27.3 0.2 18 195-212 134-151 (178)
157 PRK03681 hypA hydrogenase nick 22.7 31 0.00068 27.4 0.2 32 39-82 65-96 (114)
158 PRK14873 primosome assembly pr 22.4 41 0.00089 34.4 1.0 39 40-82 388-431 (665)
159 COG1198 PriA Primosomal protei 22.3 41 0.00089 35.1 1.1 40 40-82 440-484 (730)
160 PF10276 zf-CHCC: Zinc-finger 22.1 31 0.00067 23.3 0.1 10 44-53 29-38 (40)
161 KOG3608 Zn finger proteins [Ge 21.9 57 0.0012 32.1 1.8 67 13-94 244-313 (467)
162 COG3058 FdhE Uncharacterized p 21.7 36 0.00078 32.2 0.4 19 72-90 184-202 (308)
163 PF13719 zinc_ribbon_5: zinc-r 21.6 67 0.0015 20.7 1.6 31 45-81 3-33 (37)
164 TIGR00630 uvra excinuclease AB 21.6 48 0.001 35.3 1.4 36 42-82 248-283 (924)
165 KOG0402 60S ribosomal protein 21.6 27 0.00059 27.6 -0.3 14 39-52 31-44 (92)
166 smart00451 ZnF_U1 U1-like zinc 21.5 64 0.0014 19.4 1.4 20 45-64 4-24 (35)
167 PRK14714 DNA polymerase II lar 21.4 48 0.001 36.9 1.4 21 44-65 667-687 (1337)
168 TIGR01374 soxD sarcosine oxida 21.2 42 0.00092 26.1 0.7 14 45-59 2-15 (84)
169 PLN02751 glutamyl-tRNA(Gln) am 21.2 46 0.00099 33.6 1.1 23 63-85 83-105 (544)
170 TIGR03278 methan_mark_10 putat 21.2 40 0.00088 32.4 0.7 33 44-82 10-45 (404)
171 KOG4628 Predicted E3 ubiquitin 21.2 27 0.00059 33.4 -0.4 47 36-83 222-277 (348)
172 PF01323 DSBA: DSBA-like thior 21.0 14 0.0003 29.7 -2.1 19 42-60 5-24 (193)
173 PF14279 HNH_5: HNH endonuclea 20.6 42 0.0009 24.9 0.5 40 47-91 1-48 (71)
174 PF04981 NMD3: NMD3 family ; 20.6 56 0.0012 28.7 1.4 11 72-82 34-44 (236)
175 KOG2114 Vacuolar assembly/sort 20.5 40 0.00086 36.1 0.5 44 46-89 842-890 (933)
176 PF02934 GatB_N: GatB/GatE cat 20.4 47 0.001 31.0 1.0 24 62-85 21-44 (289)
177 PF13717 zinc_ribbon_4: zinc-r 20.3 66 0.0014 20.7 1.4 31 45-81 3-33 (36)
178 COG4391 Uncharacterized protei 20.2 46 0.00099 24.7 0.7 13 70-82 45-57 (62)
179 PF06676 DUF1178: Protein of u 20.0 48 0.001 28.1 0.9 20 63-82 8-41 (148)
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=99.77 E-value=1.8e-19 Score=125.21 Aligned_cols=53 Identities=32% Similarity=0.726 Sum_probs=51.6
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCcccccccccccccchhHhhhhhhhcc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHFMVQHA 96 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D~i~Hit~QH~ 96 (220)
+|+||||+++||+.+|+.|++++|+.+.+++|||||+.+++.||++||+.+||
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 79999999999999999999999999999999999999999999999999986
No 2
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=99.49 E-value=8e-15 Score=115.55 Aligned_cols=76 Identities=25% Similarity=0.355 Sum_probs=57.4
Q ss_pred hhhhhhh-----hhhhcCCCCcCCCCCCCCCCCCcccccccCCCCCCCCCCCcccccccccccccccCCCChhhhhhhhh
Q 027681 115 SAMLGKE-----LSSFLGSPTIVRGNAPESLPDPLLSPFLCSGTLSDTKGIQKDDCTNKFSLASDLKRYPPSSEYKLLWS 189 (220)
Q Consensus 115 ~~ll~ke-----LqsllGgs~~s~~~~sn~~pDPLLSsFi~n~~~~e~~~~e~~~~~~~~~~~~~~kr~~~~~~wk~~~~ 189 (220)
+++|+|| ||+||||+++++++++|++|||||||||||+|.++. .+..+......+++..+...+...|+...+
T Consensus 2 lsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~--~~~~~~~~~~~~~~s~~~~~~~~~~~~s~~ 79 (105)
T PF14571_consen 2 LSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEA--EEPSKSSSSSEEKKSSKKSSSEQNVKSSAD 79 (105)
T ss_pred cchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCccc--cccCCccccccccccccccchhcccccccC
Confidence 5678998 699999986677889999999999999999999884 333333333345667777778888886655
Q ss_pred HHH
Q 027681 190 QLL 192 (220)
Q Consensus 190 ~~l 192 (220)
+.|
T Consensus 80 ~~l 82 (105)
T PF14571_consen 80 SSL 82 (105)
T ss_pred CCC
Confidence 443
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=97.61 E-value=3.8e-05 Score=72.34 Aligned_cols=41 Identities=32% Similarity=0.752 Sum_probs=38.6
Q ss_pred ceecCCCCCc-cchHHHhhhhhhcccCCCccccccccccccc
Q 027681 43 ACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 43 ~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
..|.||||++ .|....+.+|+..+|+.-...+|||||+...
T Consensus 78 qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~ 119 (381)
T KOG1280|consen 78 QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANP 119 (381)
T ss_pred ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCc
Confidence 3899999998 9999999999999999999889999999984
No 4
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.74 E-value=0.011 Score=44.03 Aligned_cols=45 Identities=20% Similarity=0.459 Sum_probs=29.7
Q ss_pred CccCccc-cCCCccceecCCCCCccchH--HHhhhhhhcccCCCccccccccccccc
Q 027681 30 SIVDETE-IDDDVKACFPCPFCYLEIEA--HMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 30 ~~~de~e-~ddd~r~~F~CPfC~ed~D~--~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
..|+|++ ++|....+|||| |+..|.+ ..|. .--..+.||-|+-.+
T Consensus 7 Veiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 7 VEIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLII 54 (67)
T ss_pred EEeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEE
Confidence 3566777 445567799999 9875544 3332 223457899999875
No 5
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.35 E-value=0.021 Score=42.22 Aligned_cols=36 Identities=25% Similarity=0.561 Sum_probs=24.8
Q ss_pred CCccceecCCCCCccchH--HHhhhhhhcccCCCccccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEA--HMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~--~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
++...+|||| |+.-|.+ ..|.. --+.++||-|+-+|
T Consensus 17 e~~~ftyPCP-CGDRFeIsLeDl~~--------GE~VArCPSCSLiv 54 (67)
T COG5216 17 EEKTFTYPCP-CGDRFEISLEDLRN--------GEVVARCPSCSLIV 54 (67)
T ss_pred CCceEEecCC-CCCEeEEEHHHhhC--------CceEEEcCCceEEE
Confidence 4567899999 9865544 33322 24568899999875
No 6
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=89.89 E-value=0.18 Score=27.85 Aligned_cols=23 Identities=26% Similarity=0.595 Sum_probs=14.2
Q ss_pred ecCCCCCc-cchHHHhhhhhhccc
Q 027681 45 FPCPFCYL-EIEAHMICSHLQEEH 67 (220)
Q Consensus 45 F~CPfC~e-d~D~~~Lc~H~~eeH 67 (220)
|.||+|+. --+..+|..|+...|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 67888876 445667777776654
No 7
>PHA00732 hypothetical protein
Probab=89.42 E-value=0.33 Score=36.68 Aligned_cols=42 Identities=26% Similarity=0.729 Sum_probs=31.8
Q ss_pred ecCCCCCccc-hHHHhhhhhhcccCCCcccccccccccccchhHhhhh
Q 027681 45 FPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHF 91 (220)
Q Consensus 45 F~CPfC~ed~-D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D~i~Hi 91 (220)
|.|+.|++.| ....|..|....|.- ..|++|...-. .+..|+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~-~l~~H~ 44 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR-RLNQHF 44 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC-Chhhhh
Confidence 7899999855 678899998755542 26999998765 566666
No 8
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=88.78 E-value=0.27 Score=29.64 Aligned_cols=21 Identities=24% Similarity=0.608 Sum_probs=18.4
Q ss_pred eecCCCCCccchHHHhhhhhh
Q 027681 44 CFPCPFCYLEIEAHMICSHLQ 64 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~ 64 (220)
..+||+|++.|....|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 468999999999999999964
No 9
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.22 E-value=0.39 Score=39.41 Aligned_cols=40 Identities=23% Similarity=0.444 Sum_probs=27.3
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
+.....|.||.|+..|+...-....+ + ....+||.|...+
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l 133 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEEL 133 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEE
Confidence 44577999999988666544333322 2 3448999999986
No 10
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=88.11 E-value=0.25 Score=28.50 Aligned_cols=24 Identities=25% Similarity=0.627 Sum_probs=16.9
Q ss_pred ecCCCCCccchHHHhhhhhhcccC
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHC 68 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~ 68 (220)
|.||+|...-....|..|+...|+
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 689999763347789999888775
No 11
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=87.14 E-value=0.24 Score=48.73 Aligned_cols=35 Identities=29% Similarity=0.600 Sum_probs=30.3
Q ss_pred CCccceecCCCCCccch-HHHhhhhhhcccCCCccc
Q 027681 39 DDVKACFPCPFCYLEIE-AHMICSHLQEEHCFEMKN 73 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D-~~~Lc~H~~eeH~~e~k~ 73 (220)
++.+.-|.||+|.++|+ +..|-+|++.+|+.|-..
T Consensus 10 ~~i~egflCPiC~~dl~~~~~L~~H~d~eH~~ed~~ 45 (505)
T KOG1842|consen 10 GEILEGFLCPICLLDLPNLSALNDHLDVEHFEEDEK 45 (505)
T ss_pred chhhhcccCchHhhhhhhHHHHHHHHhhhccccchh
Confidence 56788999999988775 678999999999998764
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=86.37 E-value=0.62 Score=46.74 Aligned_cols=45 Identities=18% Similarity=0.358 Sum_probs=35.4
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCcccccccccccc-cchhHhhhhhh
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN-LGKDAAEHFMV 93 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~-vg~D~i~Hit~ 93 (220)
-+.||+|++.|....|-.|....| +...|| |... ...++..|++.
T Consensus 453 H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~t 498 (567)
T PLN03086 453 HVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQAS 498 (567)
T ss_pred CccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhc
Confidence 458999999888899999988865 678999 9754 34578888743
No 13
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=85.93 E-value=0.49 Score=34.10 Aligned_cols=27 Identities=26% Similarity=0.694 Sum_probs=17.2
Q ss_pred ccccccccccccc--chhHhhhhhhhccc
Q 027681 71 MKNAVCPLCAANL--GKDAAEHFMVQHAS 97 (220)
Q Consensus 71 ~k~vVCPVCa~~v--g~D~i~Hit~QH~~ 97 (220)
..+..||+|.+.+ ..|+-+|+.+.|+.
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 4456999999975 67999999776663
No 14
>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=83.98 E-value=0.44 Score=30.40 Aligned_cols=33 Identities=21% Similarity=0.386 Sum_probs=22.9
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
.+|.||-|+..|++..-. .+....+||.|...+
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 579999999877643211 125667899999843
No 15
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=83.78 E-value=0.6 Score=33.67 Aligned_cols=48 Identities=23% Similarity=0.582 Sum_probs=13.9
Q ss_pred cCCCCCcc-chHHHhhhhhhcccCCCcc---------------------ccccccccccc--chhHhhhhhh
Q 027681 46 PCPFCYLE-IEAHMICSHLQEEHCFEMK---------------------NAVCPLCAANL--GKDAAEHFMV 93 (220)
Q Consensus 46 ~CPfC~ed-~D~~~Lc~H~~eeH~~e~k---------------------~vVCPVCa~~v--g~D~i~Hit~ 93 (220)
.|+||... -+...|..|+...|.+... .-.|++|.... ...+..||+.
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 39999775 4578899999999987432 12399999974 4588899943
No 16
>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=83.00 E-value=0.56 Score=26.45 Aligned_cols=21 Identities=19% Similarity=0.621 Sum_probs=12.9
Q ss_pred ecCCCCCccc-hHHHhhhhhhc
Q 027681 45 FPCPFCYLEI-EAHMICSHLQE 65 (220)
Q Consensus 45 F~CPfC~ed~-D~~~Lc~H~~e 65 (220)
|.||.|++.| +...|..|+..
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 5677777643 45556666654
No 17
>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=82.55 E-value=0.43 Score=34.07 Aligned_cols=30 Identities=33% Similarity=0.520 Sum_probs=21.9
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
.|.||-|++.+++..... .-.+.||.|.+.
T Consensus 2 ~~~CP~CG~~iev~~~~~---------GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL---------GELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCcc---------CCEEeCCCCCCE
Confidence 588999999886654321 236799999886
No 18
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=82.18 E-value=0.59 Score=30.95 Aligned_cols=35 Identities=26% Similarity=0.520 Sum_probs=21.8
Q ss_pred ecCCCCCccchHHHhhhhhhcccCCCcccccccccccccchhHhh
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAE 89 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D~i~ 89 (220)
|.||.|+... + +.+ ......||+.|...+..+.+.
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 6799997633 2 122 445667999998887766554
No 19
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=81.78 E-value=0.46 Score=33.00 Aligned_cols=31 Identities=29% Similarity=0.682 Sum_probs=18.4
Q ss_pred eecCCCCCc-cchHHHhhhhhhcccCCCc---cccccccccc
Q 027681 44 CFPCPFCYL-EIEAHMICSHLQEEHCFEM---KNAVCPLCAA 81 (220)
Q Consensus 44 ~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~---k~vVCPVCa~ 81 (220)
..|||||+. .+.+.. ....+. ..+.|.-|.+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 468999975 443322 222222 4577999987
No 20
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=81.21 E-value=0.5 Score=41.22 Aligned_cols=49 Identities=20% Similarity=0.356 Sum_probs=29.0
Q ss_pred eecCCCCCccchHHHhhh--------------hhhcccCCCcccccccccccccchhHhhhhh
Q 027681 44 CFPCPFCYLEIEAHMICS--------------HLQEEHCFEMKNAVCPLCAANLGKDAAEHFM 92 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~--------------H~~eeH~~e~k~vVCPVCa~~vg~D~i~Hit 92 (220)
++.||+|+.+|....+.. |=.+.-|.==...|||-|----..+...+++
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 678999999888664433 3233333333457899998764333223443
No 21
>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=81.20 E-value=0.95 Score=44.51 Aligned_cols=50 Identities=24% Similarity=0.325 Sum_probs=35.6
Q ss_pred cceecCCCCCc-cchHHHhhhhhhcccCCCcccccccccccccchhHhhhh
Q 027681 42 KACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHF 91 (220)
Q Consensus 42 r~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D~i~Hi 91 (220)
+.--.||+|.+ -.|..++..|++++|+..-.+-.=++...+++.+-++-|
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~~w~e~I 105 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDDDWAEMI 105 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCHHHHHHH
Confidence 44678999987 899999999999999998766433344445444433333
No 22
>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=81.03 E-value=0.57 Score=29.89 Aligned_cols=24 Identities=33% Similarity=0.690 Sum_probs=12.7
Q ss_pred cCCCCCccchHHHhhhhhhcccCCCccccccccccc
Q 027681 46 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (220)
Q Consensus 46 ~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~ 81 (220)
+||.|+.++.. .|....|||-|..
T Consensus 4 ~Cp~C~se~~y------------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY------------EDGELLVCPECGH 27 (30)
T ss_dssp --TTT-----E------------E-SSSEEETTTTE
T ss_pred CCCCCCCccee------------ccCCEEeCCcccc
Confidence 69999765544 5667789999974
No 23
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=80.96 E-value=0.62 Score=34.63 Aligned_cols=32 Identities=28% Similarity=0.604 Sum_probs=21.2
Q ss_pred eecCCCCCc-cchHHHhhhhhhcccCCCcccccccccccccc
Q 027681 44 CFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 84 (220)
Q Consensus 44 ~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg 84 (220)
.-|||||+. .+++. |..-.-.++|.-|.+...
T Consensus 6 lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~~~ 38 (64)
T PRK09710 6 VKPCPFCGCPSVTVK---------AISGYYRAKCNGCESRTG 38 (64)
T ss_pred ccCCCCCCCceeEEE---------ecCceEEEEcCCCCcCcc
Confidence 468999976 44443 232234589999999743
No 24
>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=0.75 Score=31.08 Aligned_cols=32 Identities=22% Similarity=0.512 Sum_probs=22.5
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
.+|.|+-|+..|++. ....+ .....||.|...
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 589999999888853 12222 355789999983
No 25
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=80.11 E-value=0.8 Score=40.34 Aligned_cols=50 Identities=18% Similarity=0.544 Sum_probs=30.2
Q ss_pred cceecCCCCCccch--HHHhhhhh-----hcccC--------------CCcccccccccccccchhHhhhh
Q 027681 42 KACFPCPFCYLEIE--AHMICSHL-----QEEHC--------------FEMKNAVCPLCAANLGKDAAEHF 91 (220)
Q Consensus 42 r~~F~CPfC~ed~D--~~~Lc~H~-----~eeH~--------------~e~k~vVCPVCa~~vg~D~i~Hi 91 (220)
..+|.||.|.+.+. +...|-|. -.+.- ...+...||+|...++.+-+..+
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPi 86 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPI 86 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEe
Confidence 45799999966333 44557772 32211 12345689999999876444333
No 26
>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=80.03 E-value=0.9 Score=28.98 Aligned_cols=32 Identities=16% Similarity=0.243 Sum_probs=19.9
Q ss_pred ecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+.||.|+..|.+..-- .+.+...+.||.|...
T Consensus 3 ~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHH------cCCCCCEEECCCCCCE
Confidence 6799998765554322 1222346889999765
No 27
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=79.74 E-value=2.2 Score=41.39 Aligned_cols=36 Identities=22% Similarity=0.457 Sum_probs=28.3
Q ss_pred ccceecCCCCCc-cchHHHhhhhhhcccCCCcccccccccccc
Q 027681 41 VKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 41 ~r~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+.--=.|-||.. =+|-.+|..||.+.|- .|-||..+
T Consensus 217 FKGHP~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v 253 (493)
T COG5236 217 FKGHPLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMV 253 (493)
T ss_pred cCCCchhhhccceecChHHHHHHHHhhhh------hhhhhhcc
Confidence 555667999976 7899999999999874 47777654
No 28
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=79.12 E-value=1.9 Score=29.36 Aligned_cols=29 Identities=17% Similarity=0.115 Sum_probs=20.7
Q ss_pred CCccchHHHhhhhhhcccCCCcccccccccccccch
Q 027681 50 CYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 50 C~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~ 85 (220)
|+.-|+...+..++.. ...||+|...++.
T Consensus 19 ~G~v~~~~~i~~~~~~-------~~~cP~~~~~~~~ 47 (63)
T smart00504 19 SGQTYERRAIEKWLLS-------HGTDPVTGQPLTH 47 (63)
T ss_pred CCCEEeHHHHHHHHHH-------CCCCCCCcCCCCh
Confidence 3445777777777765 4689999988754
No 29
>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=75.51 E-value=0.31 Score=36.72 Aligned_cols=56 Identities=29% Similarity=0.396 Sum_probs=27.3
Q ss_pred ecCCCCCccchHHHhhhhhhcccCCCccccccccccccc------c-hhHhhhhhhhccchhhhhhc
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL------G-KDAAEHFMVQHASSLKRRRK 104 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v------g-~D~i~Hit~QH~~~fKrrrr 104 (220)
..||-|..+++..+---||+.=+..=.+.+.||-|...+ | .|+.= ||+|-+|.|+|
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC----~~c~gLiSKkr 64 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFC----NHCHGLISKKR 64 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-----TTTT-EE-TTT
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceee----ccCCceeecce
Confidence 357777666776664334333222334568899999875 2 35555 67777765544
No 30
>PHA00733 hypothetical protein
Probab=74.85 E-value=3.9 Score=33.16 Aligned_cols=48 Identities=21% Similarity=0.642 Sum_probs=33.2
Q ss_pred eecCCCCCccch-HHHhhhhhhcccCCCccccccccccccc--chhHhhhhhhhc
Q 027681 44 CFPCPFCYLEIE-AHMICSHLQEEHCFEMKNAVCPLCAANL--GKDAAEHFMVQH 95 (220)
Q Consensus 44 ~F~CPfC~ed~D-~~~Lc~H~~eeH~~e~k~vVCPVCa~~v--g~D~i~Hit~QH 95 (220)
.|.|+.|+..|. ...|-.|..- | .....|++|.... ...+..|+.--|
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 589999998665 4557788763 2 1235999998863 457888884443
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=71.87 E-value=2.3 Score=30.57 Aligned_cols=25 Identities=24% Similarity=0.759 Sum_probs=20.5
Q ss_pred ceecCCCCCccc-hHHHhhhhhhccc
Q 027681 43 ACFPCPFCYLEI-EAHMICSHLQEEH 67 (220)
Q Consensus 43 ~~F~CPfC~ed~-D~~~Lc~H~~eeH 67 (220)
..+.|++|++.| +..+|..|+...+
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 369999999877 7999999999853
No 32
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=71.65 E-value=1.4 Score=31.24 Aligned_cols=34 Identities=21% Similarity=0.489 Sum_probs=19.6
Q ss_pred ecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
+.||||++.+++. .+.-...+ ..--=|+||-..+
T Consensus 1 i~CPyCge~~~~~--iD~s~~~Q---~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEIL--IDPSAGDQ---EYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEEE--EecCCCCe---eEEeehhhcCCcc
Confidence 4699999977662 22222211 1123499987764
No 33
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=70.43 E-value=2.8 Score=28.02 Aligned_cols=29 Identities=24% Similarity=0.548 Sum_probs=18.1
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
+|.||-|+..+++... . ....||-|..++
T Consensus 3 ~y~C~~CG~~~~~~~~---------~--~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY---------G--TGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC---------C--CceECCCCCCeE
Confidence 6788888776655211 1 156788887653
No 34
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=70.41 E-value=2.2 Score=26.99 Aligned_cols=25 Identities=32% Similarity=0.814 Sum_probs=15.7
Q ss_pred ecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+.|+-|+.-+|... .+-+||+|.+.
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCCc
Confidence 56888865444322 45589999764
No 35
>PLN03086 PRLI-interacting factor K; Provisional
Probab=69.32 E-value=4.2 Score=40.99 Aligned_cols=38 Identities=21% Similarity=0.572 Sum_probs=28.4
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
..+.|| |+..+.-..|-.|+.. |+-+ +...|+.|...+
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~t-hCp~-Kpi~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQAS-TCPL-RLITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhhc-cCCC-CceeCCCCCCcc
Confidence 457888 8877788888888754 5553 677888888776
No 36
>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=69.27 E-value=3.1 Score=35.19 Aligned_cols=54 Identities=24% Similarity=0.438 Sum_probs=32.6
Q ss_pred ceecCCC----CCccchHHHhhhhhhcccCCCcccccccc----cccc-cchhHhhhhhhhccchh
Q 027681 43 ACFPCPF----CYLEIEAHMICSHLQEEHCFEMKNAVCPL----CAAN-LGKDAAEHFMVQHASSL 99 (220)
Q Consensus 43 ~~F~CPf----C~ed~D~~~Lc~H~~eeH~~e~k~vVCPV----Ca~~-vg~D~i~Hit~QH~~~f 99 (220)
-.|||+| |.+.+-......|.++ -.+ ++--||+ |.-. ...++..|++..|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~~-C~~--~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEEE-CPF--RPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHHT--TT--SEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhcc-CCC--cCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 3799999 9888988999999654 333 4567998 6543 45699999999998744
No 37
>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=69.06 E-value=1.5 Score=37.38 Aligned_cols=53 Identities=19% Similarity=0.352 Sum_probs=26.4
Q ss_pred cceecCCCCCccchHHHhhhhhhcccCCCcccccccccccccch-hHhhhhhhhcc
Q 027681 42 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK-DAAEHFMVQHA 96 (220)
Q Consensus 42 r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~-D~i~Hit~QH~ 96 (220)
+-.|.||.|+..+...++.. .+.-........||-|...... -+...++++-|
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~~~~~l~Nql~l~iR 69 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPLSPASLVNQLELQIR 69 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B--HHHHHHHHHHHHH
T ss_pred ceEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcCCHHHHHHHHHHHHH
Confidence 35899999999888888655 2222233456789999997654 44444433333
No 38
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=68.58 E-value=1.2 Score=43.01 Aligned_cols=36 Identities=25% Similarity=0.635 Sum_probs=22.1
Q ss_pred CCCCCccchHHH-----------hhhhhhcccCCCccccccccccccc
Q 027681 47 CPFCYLEIEAHM-----------ICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 47 CPfC~ed~D~~~-----------Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
||.|-|.+|+.. +|..|-. |--+.-||-||.|..+.
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~~-~irq~lngrcpacrr~y 63 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCYN-NIRQNLNGRCPACRRKY 63 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHHH-HHHhhccCCChHhhhhc
Confidence 777777666642 2333222 22334789999999873
No 39
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=68.58 E-value=2.1 Score=33.98 Aligned_cols=38 Identities=16% Similarity=0.398 Sum_probs=22.5
Q ss_pred ccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccccchh
Q 027681 41 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKD 86 (220)
Q Consensus 41 ~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D 86 (220)
+...|.||+|++ .-+. +.-.+ ---..+||+|-..-+..
T Consensus 18 lpt~f~CP~Cge-~~v~-----v~~~k--~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 18 LPKIFECPRCGK-VSIS-----VKIKK--NIAIITCGNCGLYTEFE 55 (99)
T ss_pred CCcEeECCCCCC-eEee-----eecCC--CcceEECCCCCCccCEE
Confidence 345899999984 1111 11111 13347999999886653
No 40
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=67.36 E-value=4.4 Score=37.67 Aligned_cols=37 Identities=22% Similarity=0.615 Sum_probs=23.8
Q ss_pred cceecCCCCCc-cchHHHhhhhhhcccCCCcccccccccccc
Q 027681 42 KACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 42 r~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+..|.||+|++ .+-+.+|--||.. |.. .-+|+||.+.
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirT-H~l---~c~C~iCGKa 196 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRT-HTL---PCECGICGKA 196 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhc-cCC---Cccccccccc
Confidence 56677777766 6777777777765 432 3456666655
No 41
>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=67.17 E-value=4.3 Score=33.97 Aligned_cols=35 Identities=26% Similarity=0.475 Sum_probs=25.5
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
+.....|.||-|..-|...+-.. .+-.||+|...+
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAML 138 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEe
Confidence 44567899999987555555443 256999999985
No 42
>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=66.91 E-value=3.4 Score=28.52 Aligned_cols=16 Identities=31% Similarity=0.822 Sum_probs=8.1
Q ss_pred CCCCC-c---cchHHHhhhh
Q 027681 47 CPFCY-L---EIEAHMICSH 62 (220)
Q Consensus 47 CPfC~-e---d~D~~~Lc~H 62 (220)
||||. . +|-..+|..|
T Consensus 1 CP~C~~kkk~~Y~~~~LlqH 20 (43)
T PF03470_consen 1 CPFCPGKKKQDYKYRELLQH 20 (43)
T ss_pred CCCCCCCCCcceehhHHHHH
Confidence 66662 1 4555555555
No 43
>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=1.8 Score=28.76 Aligned_cols=31 Identities=26% Similarity=0.465 Sum_probs=22.5
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCccccccccccc
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~ 81 (220)
.+|.|+-|+..|++..- + .+...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~---~-----~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQS---I-----SEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEE---c-----CCCCCCcCCCCCC
Confidence 58999999987775421 1 1256789999988
No 44
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=66.84 E-value=4.8 Score=34.43 Aligned_cols=35 Identities=23% Similarity=0.524 Sum_probs=24.3
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
+.....|.||-|+.-|....-.. ..-.||+|...+
T Consensus 112 e~~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEML 146 (178)
T ss_pred ccCCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCC
Confidence 34457999999987444444322 256999999986
No 45
>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=65.52 E-value=4.3 Score=24.70 Aligned_cols=19 Identities=42% Similarity=1.032 Sum_probs=8.2
Q ss_pred cCCCCCccchHHHhhhhhh
Q 027681 46 PCPFCYLEIEAHMICSHLQ 64 (220)
Q Consensus 46 ~CPfC~ed~D~~~Lc~H~~ 64 (220)
+||-|.+.+....+-.|++
T Consensus 3 ~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREVPENLINSHLD 21 (26)
T ss_pred cCCCCcCcccHHHHHHHHH
Confidence 3444444444444444443
No 46
>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=64.25 E-value=3.7 Score=26.38 Aligned_cols=26 Identities=31% Similarity=0.750 Sum_probs=16.9
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
.+.|+-|+.-++... ..-+||||.+.
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 477899976444321 23499999875
No 47
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=64.05 E-value=3.3 Score=28.20 Aligned_cols=45 Identities=31% Similarity=0.612 Sum_probs=29.4
Q ss_pred eecCCC--CCccchHHHhhhhhhcccCCCcccccccc----cccccch-hHhhh
Q 027681 44 CFPCPF--CYLEIEAHMICSHLQEEHCFEMKNAVCPL----CAANLGK-DAAEH 90 (220)
Q Consensus 44 ~F~CPf--C~ed~D~~~Lc~H~~eeH~~e~k~vVCPV----Ca~~vg~-D~i~H 90 (220)
..+||+ |.+.+-...|-.|+..+=+. +.+.||. |..++.. ++.+|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~~--~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECPK--RPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTSTT--SEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCCC--CcEECCCCCCCCCCccchhHHhCC
Confidence 578999 77789999999999964433 5779999 9998654 44443
No 48
>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=62.00 E-value=3.2 Score=31.55 Aligned_cols=35 Identities=20% Similarity=0.567 Sum_probs=13.3
Q ss_pred ccceecCCCCC-c-cchHHHhhhhhhcccCCCcccccccccccc
Q 027681 41 VKACFPCPFCY-L-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 41 ~r~~F~CPfC~-e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+...|.||||+ + -+.+. -......-.+.|-+|...
T Consensus 19 l~~~F~CPfC~~~~sV~v~-------idkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVK-------IDKKEGIGILSCRVCGES 55 (81)
T ss_dssp -SS----TTT--SS-EEEE-------EETTTTEEEEEESSS--E
T ss_pred CCceEcCCcCCCCCeEEEE-------EEccCCEEEEEecCCCCe
Confidence 34689999997 4 22211 111122334679999765
No 49
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.67 E-value=4.4 Score=35.73 Aligned_cols=44 Identities=20% Similarity=0.676 Sum_probs=25.6
Q ss_pred cceecCCCCCccchHH----HhhhhhhcccCC---Ccccccccccccccch
Q 027681 42 KACFPCPFCYLEIEAH----MICSHLQEEHCF---EMKNAVCPLCAANLGK 85 (220)
Q Consensus 42 r~~F~CPfC~ed~D~~----~Lc~H~~eeH~~---e~k~vVCPVCa~~vg~ 85 (220)
.+.|.||-|-..+..- .=|=|+-=.-|. -.+..+||+|..++..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 3579999995443332 233333222222 1245789999998765
No 50
>PHA02768 hypothetical protein; Provisional
Probab=60.27 E-value=6.9 Score=28.20 Aligned_cols=34 Identities=24% Similarity=0.501 Sum_probs=21.4
Q ss_pred eecCCCCCccc-hHHHhhhhhhcccCCCccccccccccc
Q 027681 44 CFPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAA 81 (220)
Q Consensus 44 ~F~CPfC~ed~-D~~~Lc~H~~eeH~~e~k~vVCPVCa~ 81 (220)
-|.||.|++.| ..+.|..|... |. ++--|..|..
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~-H~---k~~kc~~C~k 39 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRK-HN---TNLKLSNCKR 39 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHh-cC---CcccCCcccc
Confidence 37788887744 45677788777 44 3445555544
No 51
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.82 E-value=3.6 Score=37.80 Aligned_cols=13 Identities=23% Similarity=0.795 Sum_probs=9.7
Q ss_pred ceecCCCCCccch
Q 027681 43 ACFPCPFCYLEIE 55 (220)
Q Consensus 43 ~~F~CPfC~ed~D 55 (220)
.++.||+|..-|-
T Consensus 18 k~ieCPvC~tkFk 30 (267)
T COG1655 18 KTIECPVCNTKFK 30 (267)
T ss_pred ceeccCcccchhh
Confidence 4788999976543
No 52
>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=59.70 E-value=3.9 Score=28.19 Aligned_cols=9 Identities=33% Similarity=0.726 Sum_probs=6.9
Q ss_pred ccccccccc
Q 027681 75 VCPLCAANL 83 (220)
Q Consensus 75 VCPVCa~~v 83 (220)
.|+.|.+..
T Consensus 28 ~C~~Cga~~ 36 (53)
T TIGR03655 28 ECSTCGASG 36 (53)
T ss_pred ECCCCCCCc
Confidence 699888763
No 53
>PRK12496 hypothetical protein; Provisional
Probab=59.39 E-value=3.7 Score=34.66 Aligned_cols=29 Identities=17% Similarity=0.388 Sum_probs=20.0
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCcccccccccccccc
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 84 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg 84 (220)
=.+.|+.|+..|+.. ....+||||...+.
T Consensus 126 w~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~~ 154 (164)
T PRK12496 126 WRKVCKGCKKKYPED-------------YPDDVCEICGSPVK 154 (164)
T ss_pred eeEECCCCCccccCC-------------CCCCcCCCCCChhh
Confidence 358899999877531 12248999987653
No 54
>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=58.90 E-value=3.5 Score=24.59 Aligned_cols=11 Identities=27% Similarity=0.975 Sum_probs=8.9
Q ss_pred eecCCCCCccc
Q 027681 44 CFPCPFCYLEI 54 (220)
Q Consensus 44 ~F~CPfC~ed~ 54 (220)
-|.||+|+..|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 39999998755
No 55
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=58.84 E-value=2.5 Score=33.26 Aligned_cols=16 Identities=38% Similarity=0.727 Sum_probs=12.7
Q ss_pred cCCCccceecCCCCCc
Q 027681 37 IDDDVKACFPCPFCYL 52 (220)
Q Consensus 37 ~ddd~r~~F~CPfC~e 52 (220)
.|....+.|.||||+.
T Consensus 29 ie~~q~a~y~CpfCgk 44 (90)
T PTZ00255 29 IEISQHAKYFCPFCGK 44 (90)
T ss_pred HHHHHhCCccCCCCCC
Confidence 3456788999999975
No 56
>PF12773 DZR: Double zinc ribbon
Probab=58.71 E-value=5.2 Score=26.63 Aligned_cols=28 Identities=25% Similarity=0.569 Sum_probs=18.3
Q ss_pred cCCCCCccchHHHhhhhhhcccCCCcccccccccccccch
Q 027681 46 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 46 ~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~ 85 (220)
.||.|+..+. ..+....+||.|...+..
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAENPP 41 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCCCcC
Confidence 3777766555 344556788888876543
No 57
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=56.05 E-value=6.8 Score=29.95 Aligned_cols=26 Identities=35% Similarity=0.897 Sum_probs=16.0
Q ss_pred ecCCCCCc-cchHHHhhhhhhcccCCCccccccccccc
Q 027681 45 FPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (220)
Q Consensus 45 F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~ 81 (220)
|+||-|+. -|+..+ +..--+||||-=
T Consensus 2 ~~CPCCg~~Tl~~~~-----------~~~ydIC~VC~W 28 (78)
T PF14206_consen 2 YPCPCCGYYTLEERG-----------EGTYDICPVCFW 28 (78)
T ss_pred ccCCCCCcEEeccCC-----------CcCceECCCCCc
Confidence 78999964 444321 222459999963
No 58
>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=53.14 E-value=8 Score=23.65 Aligned_cols=12 Identities=42% Similarity=0.977 Sum_probs=9.8
Q ss_pred ccceecCCCCCc
Q 027681 41 VKACFPCPFCYL 52 (220)
Q Consensus 41 ~r~~F~CPfC~e 52 (220)
.-..|+||-|++
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 456899999986
No 59
>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=52.97 E-value=8.2 Score=25.08 Aligned_cols=22 Identities=27% Similarity=0.567 Sum_probs=12.3
Q ss_pred ceecCCCCCccchHHHhhhhhh
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQ 64 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~ 64 (220)
++|.||-|+..+-..-+--|++
T Consensus 3 ~~~~C~nC~R~v~a~RfA~HLe 24 (33)
T PF08209_consen 3 PYVECPNCGRPVAASRFAPHLE 24 (33)
T ss_dssp -EEE-TTTSSEEEGGGHHHHHH
T ss_pred CeEECCCCcCCcchhhhHHHHH
Confidence 3566666666666666666655
No 60
>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=52.94 E-value=6.9 Score=26.89 Aligned_cols=11 Identities=45% Similarity=1.177 Sum_probs=4.3
Q ss_pred cccccccccch
Q 027681 75 VCPLCAANLGK 85 (220)
Q Consensus 75 VCPVCa~~vg~ 85 (220)
+||||...++.
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 66666666544
No 61
>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=52.46 E-value=3.5 Score=32.49 Aligned_cols=16 Identities=44% Similarity=0.831 Sum_probs=12.5
Q ss_pred cCCCccceecCCCCCc
Q 027681 37 IDDDVKACFPCPFCYL 52 (220)
Q Consensus 37 ~ddd~r~~F~CPfC~e 52 (220)
.|....+.|.||||+.
T Consensus 28 ie~~q~a~y~CpfCgk 43 (91)
T TIGR00280 28 IEIQQKAKYVCPFCGK 43 (91)
T ss_pred HHHHHhcCccCCCCCC
Confidence 3456788999999975
No 62
>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=51.93 E-value=6.2 Score=31.41 Aligned_cols=31 Identities=23% Similarity=0.415 Sum_probs=23.2
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
++.+..+.|+-|+..+..... ...||-|...
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 65 EDEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred EeeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 356778999999887766533 3579999874
No 63
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=51.60 E-value=3.8 Score=32.24 Aligned_cols=16 Identities=31% Similarity=0.758 Sum_probs=12.4
Q ss_pred cCCCccceecCCCCCc
Q 027681 37 IDDDVKACFPCPFCYL 52 (220)
Q Consensus 37 ~ddd~r~~F~CPfC~e 52 (220)
.|....+.|.||||+.
T Consensus 29 ie~~q~a~y~CpfCgk 44 (90)
T PRK03976 29 IEEKMRAKHVCPVCGR 44 (90)
T ss_pred HHHHHhcCccCCCCCC
Confidence 3456788999999965
No 64
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=51.38 E-value=6.4 Score=41.44 Aligned_cols=41 Identities=22% Similarity=0.445 Sum_probs=35.6
Q ss_pred cceecCCCCCc-cchHHHhhhhhhcccCCCcccccccccccc
Q 027681 42 KACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 42 r~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
-+...||||.. .-.+..|-.|+.-.|--..-|.-|+.|...
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsyt 249 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYT 249 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhh
Confidence 45678999988 446789999999999998889999999986
No 65
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=51.20 E-value=11 Score=27.60 Aligned_cols=34 Identities=26% Similarity=0.614 Sum_probs=22.8
Q ss_pred CccceecCCCCCcc-chHHHhhhhhhcccCCCcccccccccc
Q 027681 40 DVKACFPCPFCYLE-IEAHMICSHLQEEHCFEMKNAVCPLCA 80 (220)
Q Consensus 40 d~r~~F~CPfC~ed-~D~~~Lc~H~~eeH~~e~k~vVCPVCa 80 (220)
|.-..|.||-|++. +-. |..|.. .+..-+||-|-
T Consensus 21 ~~~~~F~CPnCG~~~I~R---C~~CRk----~~~~Y~CP~CG 55 (59)
T PRK14890 21 EKAVKFLCPNCGEVIIYR---CEKCRK----QSNPYTCPKCG 55 (59)
T ss_pred CccCEeeCCCCCCeeEee---chhHHh----cCCceECCCCC
Confidence 34579999999885 443 444443 24557899885
No 66
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=51.14 E-value=21 Score=25.81 Aligned_cols=37 Identities=22% Similarity=0.319 Sum_probs=23.4
Q ss_pred ceecCCCCC------------ccchHHHhhhhhhcccCCCcccccccccccccch
Q 027681 43 ACFPCPFCY------------LEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 43 ~~F~CPfC~------------ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~ 85 (220)
.+|.||.|+ .-||...+-.++.. ...+||+|...++.
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCCc
Confidence 467777664 34677777777766 67899999887765
No 67
>PF13395 HNH_4: HNH endonuclease
Probab=50.45 E-value=8 Score=26.70 Aligned_cols=14 Identities=29% Similarity=0.778 Sum_probs=12.1
Q ss_pred CCCCCccchHHHhh
Q 027681 47 CPFCYLEIEAHMIC 60 (220)
Q Consensus 47 CPfC~ed~D~~~Lc 60 (220)
||||++.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999988764
No 68
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=49.96 E-value=6.9 Score=31.88 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=8.9
Q ss_pred cccccccccccc
Q 027681 71 MKNAVCPLCAAN 82 (220)
Q Consensus 71 ~k~vVCPVCa~~ 82 (220)
....|||-|+.-
T Consensus 17 g~~~iCpeC~~E 28 (109)
T TIGR00686 17 GTQLICPSCLYE 28 (109)
T ss_pred CCeeECcccccc
Confidence 445789999875
No 69
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=49.32 E-value=9.4 Score=39.05 Aligned_cols=54 Identities=28% Similarity=0.518 Sum_probs=35.6
Q ss_pred cCCCccceecCCCCCc---cchHHHhhhh-----hh---cccCCCcccccccccccccchhHhhhh
Q 027681 37 IDDDVKACFPCPFCYL---EIEAHMICSH-----LQ---EEHCFEMKNAVCPLCAANLGKDAAEHF 91 (220)
Q Consensus 37 ~ddd~r~~F~CPfC~e---d~D~~~Lc~H-----~~---eeH~~e~k~vVCPVCa~~vg~D~i~Hi 91 (220)
.++|...+..|-+|.+ ++ +.+=|.| |. -+--.+..|+.||+|...++-|+-+|-
T Consensus 529 ~~~enk~~~~C~lc~d~aed~-i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 529 LPDENKGEVECGLCHDPAEDY-IESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred CCccccCceeecccCChhhhh-HhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 4567777888999953 33 2233333 22 123457788999999999888776665
No 70
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=48.83 E-value=6.9 Score=38.43 Aligned_cols=43 Identities=26% Similarity=0.481 Sum_probs=28.2
Q ss_pred CccccCCCccceecCCCCCc---cchHHHhhhhhhcccCCCcccccccccccc
Q 027681 33 DETEIDDDVKACFPCPFCYL---EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 33 de~e~ddd~r~~F~CPfC~e---d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
++.+.++..++.|.||+|.. .+|...|..- +...-.|-.|..-
T Consensus 117 ed~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~-------~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 117 EDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDN-------ETGEFHCENCGGE 162 (436)
T ss_pred HHHhhhccccccccCCccccchhhhHHHHhhcc-------cCceEEEecCCCc
Confidence 34445677899999999965 5666666553 2233467777654
No 71
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=48.45 E-value=8.7 Score=24.90 Aligned_cols=26 Identities=27% Similarity=0.474 Sum_probs=12.8
Q ss_pred cceecCCCCCccchH-----HHhhhhhhccc
Q 027681 42 KACFPCPFCYLEIEA-----HMICSHLQEEH 67 (220)
Q Consensus 42 r~~F~CPfC~ed~D~-----~~Lc~H~~eeH 67 (220)
.....|-||...+.. ..|..|+...|
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 345557777665444 36666665444
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.77 E-value=11 Score=25.63 Aligned_cols=28 Identities=21% Similarity=0.392 Sum_probs=20.2
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
.|.|.-|+.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 57888998877754 23557899997664
No 73
>PRK12495 hypothetical protein; Provisional
Probab=47.63 E-value=9.8 Score=34.49 Aligned_cols=30 Identities=20% Similarity=0.331 Sum_probs=22.2
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCcccccccccccccch
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~ 85 (220)
..|.||.|+..|- .+ ....+||+|-..+..
T Consensus 41 sa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIF------------RH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCccc------------CC-CCeeECCCCCCcccc
Confidence 4688999988665 22 456789999988754
No 74
>smart00507 HNHc HNH nucleases.
Probab=47.41 E-value=4.5 Score=25.48 Aligned_cols=21 Identities=14% Similarity=0.316 Sum_probs=13.9
Q ss_pred ecCCCCCccchHHHhhhhhhc
Q 027681 45 FPCPFCYLEIEAHMICSHLQE 65 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~e 65 (220)
+.|+||++.++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 789999886654334555554
No 75
>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=47.15 E-value=7.1 Score=30.88 Aligned_cols=31 Identities=29% Similarity=0.505 Sum_probs=20.3
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+..+..+.|+-|+.+|++..... .||-|...
T Consensus 65 e~~p~~~~C~~Cg~~~~~~~~~~-------------~CP~Cgs~ 95 (113)
T PF01155_consen 65 EEVPARARCRDCGHEFEPDEFDF-------------SCPRCGSP 95 (113)
T ss_dssp EEE--EEEETTTS-EEECHHCCH-------------H-SSSSSS
T ss_pred EecCCcEECCCCCCEEecCCCCC-------------CCcCCcCC
Confidence 45678999999998887765442 39999886
No 76
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=47.08 E-value=8.6 Score=30.76 Aligned_cols=9 Identities=44% Similarity=1.331 Sum_probs=7.3
Q ss_pred eecCCCCCc
Q 027681 44 CFPCPFCYL 52 (220)
Q Consensus 44 ~F~CPfC~e 52 (220)
-++||||++
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 468999987
No 77
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=46.71 E-value=12 Score=30.89 Aligned_cols=40 Identities=28% Similarity=0.446 Sum_probs=29.3
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCcccccccccccccchhH
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDA 87 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D~ 87 (220)
....|.-|...++...+...+..+... .||.|...+-.|+
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~~~-----~C~~C~~~lrp~v 143 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEEPP-----RCPKCGGLLRPDV 143 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTSSC-----BCTTTSCBEEEEE
T ss_pred ceeeecCCCccccchhhcccccccccc-----cccccCccCCCCe
Confidence 368999999988888777666554333 9999999754443
No 78
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=46.41 E-value=16 Score=25.78 Aligned_cols=41 Identities=17% Similarity=0.335 Sum_probs=29.1
Q ss_pred CccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccccchhHhhhh
Q 027681 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHF 91 (220)
Q Consensus 40 d~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D~i~Hi 91 (220)
+....=.||.|+.-... +...+..+||.|......|..+=+
T Consensus 24 ~~~TSq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~rD~naA~ 64 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMDRDVNAAR 64 (69)
T ss_pred CCCCccCccCccccccc-----------ccccceEEcCCCCCEECcHHHHHH
Confidence 44467789999763222 555677899999998888876644
No 79
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=44.69 E-value=9.3 Score=30.36 Aligned_cols=31 Identities=29% Similarity=0.396 Sum_probs=22.0
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
++.+..+.|+-|+..+.+.. ....||-|...
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred EeeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 45677899999987665433 33469999864
No 80
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=44.60 E-value=13 Score=36.97 Aligned_cols=42 Identities=24% Similarity=0.487 Sum_probs=27.6
Q ss_pred cceecCCCCCccchHH--HhhhhhhcccCCCcccccccccccccch
Q 027681 42 KACFPCPFCYLEIEAH--MICSHLQEEHCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 42 r~~F~CPfC~ed~D~~--~Lc~H~~eeH~~e~k~vVCPVCa~~vg~ 85 (220)
+-..+||-|++.+.+. .|.- +++...+.--.+||-|...+..
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w--~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKW--DKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEEccCCCCCCCccccccceee--cCCCCccceEEECCCCcCCCCH
Confidence 6789999998754433 3322 2222444555789999998876
No 81
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=44.29 E-value=14 Score=22.16 Aligned_cols=10 Identities=50% Similarity=0.923 Sum_probs=6.4
Q ss_pred ecCCCCCccc
Q 027681 45 FPCPFCYLEI 54 (220)
Q Consensus 45 F~CPfC~ed~ 54 (220)
-.||.|+..+
T Consensus 3 ~~Cp~Cg~~~ 12 (26)
T PF13248_consen 3 MFCPNCGAEI 12 (26)
T ss_pred CCCcccCCcC
Confidence 3588886644
No 82
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=44.26 E-value=15 Score=24.87 Aligned_cols=26 Identities=19% Similarity=0.433 Sum_probs=17.4
Q ss_pred ceecCCCCCccchHH------HhhhhhhcccC
Q 027681 43 ACFPCPFCYLEIEAH------MICSHLQEEHC 68 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~------~Lc~H~~eeH~ 68 (220)
+.-.|-+|...+... .|..|+...||
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 566688887766543 67777766555
No 83
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.19 E-value=13 Score=30.50 Aligned_cols=43 Identities=26% Similarity=0.451 Sum_probs=24.2
Q ss_pred CccceecCCCCCccchHHHhhhhhhcc-----cCCC---cccccccccccc
Q 027681 40 DVKACFPCPFCYLEIEAHMICSHLQEE-----HCFE---MKNAVCPLCAAN 82 (220)
Q Consensus 40 d~r~~F~CPfC~ed~D~~~Lc~H~~ee-----H~~e---~k~vVCPVCa~~ 82 (220)
..+..+.|+-|+..+....-..+++.+ |-.. .....||.|...
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 566889999998766554211111110 1111 234679999864
No 84
>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=42.98 E-value=14 Score=26.10 Aligned_cols=44 Identities=23% Similarity=0.431 Sum_probs=26.7
Q ss_pred cCccccC-CCccceecCCCCCc--cchHHHhhhhhhcccCCCcccccccccccccc
Q 027681 32 VDETEID-DDVKACFPCPFCYL--EIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 84 (220)
Q Consensus 32 ~de~e~d-dd~r~~F~CPfC~e--d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg 84 (220)
++|++.+ ++....++|+ |+- .+....|-.+ .--+.|+-|+-.+-
T Consensus 5 l~d~~~~~~~~~~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 5 LDDMEFDEEEGVYSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIR 51 (55)
T ss_dssp TTTSEEETTTTEEEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEE
T ss_pred hhhceecCCCCEEEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEE
Confidence 4555433 3345799996 965 5555555554 34477999987653
No 85
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=42.96 E-value=14 Score=22.61 Aligned_cols=8 Identities=50% Similarity=1.173 Sum_probs=4.4
Q ss_pred CCCCCccc
Q 027681 47 CPFCYLEI 54 (220)
Q Consensus 47 CPfC~ed~ 54 (220)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 56665544
No 86
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=42.93 E-value=12 Score=30.37 Aligned_cols=37 Identities=24% Similarity=0.510 Sum_probs=21.6
Q ss_pred ccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 41 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 41 ~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+.-+|.||+|+-+-=.+-++ .-..---+++|-+|-..
T Consensus 19 L~k~FtCp~Cghe~vs~ctv-----kk~~~~g~~~Cg~CGls 55 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTV-----KKTVNIGTAVCGNCGLS 55 (104)
T ss_pred CCceEecCccCCeeeeEEEE-----EecCceeEEEcccCcce
Confidence 44589999997532222111 11223345789999876
No 87
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=41.90 E-value=17 Score=31.29 Aligned_cols=25 Identities=36% Similarity=0.822 Sum_probs=17.5
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
.+.||-|+-- |-. -.+.+||||-+.
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 8999999531 111 345799999875
No 88
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=41.78 E-value=16 Score=31.00 Aligned_cols=31 Identities=29% Similarity=0.541 Sum_probs=18.4
Q ss_pred cCCCCCccchHHHhhhhhhcccCCCcccc-----cccccccc
Q 027681 46 PCPFCYLEIEAHMICSHLQEEHCFEMKNA-----VCPLCAAN 82 (220)
Q Consensus 46 ~CPfC~ed~D~~~Lc~H~~eeH~~e~k~v-----VCPVCa~~ 82 (220)
.||||+... .|+.+.-.....|+ -||-|...
T Consensus 2 ~cp~c~~~~------~~~~~s~~~~~~~~~~~~~~c~~c~~~ 37 (154)
T PRK00464 2 RCPFCGHPD------TRVIDSRPAEDGNAIRRRRECLACGKR 37 (154)
T ss_pred cCCCCCCCC------CEeEeccccCCCCceeeeeeccccCCc
Confidence 699997533 12333333444333 49999887
No 89
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=41.51 E-value=5.2 Score=25.69 Aligned_cols=35 Identities=20% Similarity=0.545 Sum_probs=13.9
Q ss_pred CCCCCccchHH--Hhhhhhhccc---CCCccc--cccccccc
Q 027681 47 CPFCYLEIEAH--MICSHLQEEH---CFEMKN--AVCPLCAA 81 (220)
Q Consensus 47 CPfC~ed~D~~--~Lc~H~~eeH---~~e~k~--vVCPVCa~ 81 (220)
|++|++.+... --+.|+.... ..+..| .+|+.|-.
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~ 42 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHR 42 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHH
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHH
Confidence 88898766554 2344444333 223333 45666644
No 90
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=41.49 E-value=9.7 Score=28.20 Aligned_cols=24 Identities=29% Similarity=0.462 Sum_probs=16.7
Q ss_pred ccccccc--cchhHhhhhhhhccchh
Q 027681 76 CPLCAAN--LGKDAAEHFMVQHASSL 99 (220)
Q Consensus 76 CPVCa~~--vg~D~i~Hit~QH~~~f 99 (220)
||-|.+- -..|.++|..--|+++|
T Consensus 20 CPRC~~~FR~~K~Y~RHVNKaH~~~~ 45 (65)
T COG4049 20 CPRCGMVFRRRKDYIRHVNKAHGWLF 45 (65)
T ss_pred CCchhHHHHHhHHHHHHhhHHhhhhh
Confidence 4444442 35678999988899988
No 91
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=41.45 E-value=9.6 Score=22.63 Aligned_cols=7 Identities=57% Similarity=1.232 Sum_probs=3.7
Q ss_pred CCCCCcc
Q 027681 47 CPFCYLE 53 (220)
Q Consensus 47 CPfC~ed 53 (220)
||.|+.+
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 5666543
No 92
>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=41.42 E-value=11 Score=26.10 Aligned_cols=14 Identities=29% Similarity=0.771 Sum_probs=7.9
Q ss_pred CCccceecCCCCCc
Q 027681 39 DDVKACFPCPFCYL 52 (220)
Q Consensus 39 dd~r~~F~CPfC~e 52 (220)
+++..+|.||-|+.
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 46677888888854
No 93
>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=40.38 E-value=5.4 Score=31.37 Aligned_cols=15 Identities=33% Similarity=0.773 Sum_probs=11.0
Q ss_pred CCCccceecCCCCCc
Q 027681 38 DDDVKACFPCPFCYL 52 (220)
Q Consensus 38 ddd~r~~F~CPfC~e 52 (220)
|......|.||||+.
T Consensus 29 e~~q~~ky~Cp~Cgk 43 (90)
T PF01780_consen 29 EISQHAKYTCPFCGK 43 (90)
T ss_dssp HHHHHS-BEESSSSS
T ss_pred HHHHhCCCcCCCCCC
Confidence 345678999999976
No 94
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=40.21 E-value=26 Score=25.94 Aligned_cols=35 Identities=31% Similarity=0.624 Sum_probs=21.2
Q ss_pred CCccceecCCCCCc-cchHHHhhhhhhcccCCCcccccccccc
Q 027681 39 DDVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCA 80 (220)
Q Consensus 39 dd~r~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa 80 (220)
+|--..|+||-|++ .+-.-.-|.- -.+.-+||-|-
T Consensus 22 ~e~~v~F~CPnCGe~~I~Rc~~CRk-------~g~~Y~Cp~CG 57 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYRCAKCRK-------LGNPYRCPKCG 57 (61)
T ss_pred CCceeEeeCCCCCceeeehhhhHHH-------cCCceECCCcC
Confidence 35567899999996 5443333321 13345888884
No 95
>PF15616 TerY-C: TerY-C metal binding domain
Probab=39.46 E-value=10 Score=31.60 Aligned_cols=42 Identities=21% Similarity=0.515 Sum_probs=28.6
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCC-cccccccccccccchhH
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFE-MKNAVCPLCAANLGKDA 87 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e-~k~vVCPVCa~~vg~D~ 87 (220)
.=.||+|+..+-++ +| =|-.-|+++ ...++||-|-.......
T Consensus 77 ~PgCP~CGn~~~fa-~C-~CGkl~Ci~g~~~~~CPwCg~~g~~~~ 119 (131)
T PF15616_consen 77 APGCPHCGNQYAFA-VC-GCGKLFCIDGEGEVTCPWCGNEGSFGA 119 (131)
T ss_pred CCCCCCCcChhcEE-Ee-cCCCEEEeCCCCCEECCCCCCeeeecc
Confidence 46799997654433 23 477778854 45699999998754433
No 96
>smart00355 ZnF_C2H2 zinc finger.
Probab=39.38 E-value=24 Score=18.97 Aligned_cols=20 Identities=20% Similarity=0.556 Sum_probs=10.9
Q ss_pred ecCCCCCccc-hHHHhhhhhh
Q 027681 45 FPCPFCYLEI-EAHMICSHLQ 64 (220)
Q Consensus 45 F~CPfC~ed~-D~~~Lc~H~~ 64 (220)
|.|+.|+..| ....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 4577776533 3445556654
No 97
>PRK11595 DNA utilization protein GntX; Provisional
Probab=39.32 E-value=15 Score=31.84 Aligned_cols=35 Identities=23% Similarity=0.477 Sum_probs=21.0
Q ss_pred cCCCCCccchH--HHhhhhhhcccCCCcccccccccccc
Q 027681 46 PCPFCYLEIEA--HMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 46 ~CPfC~ed~D~--~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
.|+.|++.+.. ..||.+|.+.=++- ...||.|...
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg~~ 43 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCGLP 43 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCCCc
Confidence 38888765533 35788886653331 2467777654
No 98
>PRK03922 hypothetical protein; Provisional
Probab=39.18 E-value=13 Score=30.43 Aligned_cols=15 Identities=20% Similarity=0.430 Sum_probs=11.6
Q ss_pred eecCCCCCccchHHH
Q 027681 44 CFPCPFCYLEIEAHM 58 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~ 58 (220)
.-.||+|+++||-.-
T Consensus 49 ~~~cP~cge~~~~af 63 (113)
T PRK03922 49 LTICPKCGEPFDSAF 63 (113)
T ss_pred cccCCCCCCcCCcEE
Confidence 457999999988543
No 99
>PRK00420 hypothetical protein; Validated
Probab=39.07 E-value=20 Score=29.14 Aligned_cols=27 Identities=26% Similarity=0.540 Sum_probs=17.5
Q ss_pred ecCCCCCccchHHHhhhhhhcccCCCccccccccccccc
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
-.||.|+..+= . +.....+||+|..-+
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 56999975321 1 123457999999864
No 100
>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=38.83 E-value=20 Score=20.70 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=14.6
Q ss_pred ecCCCCCccc-hHHHhhhhhhcc
Q 027681 45 FPCPFCYLEI-EAHMICSHLQEE 66 (220)
Q Consensus 45 F~CPfC~ed~-D~~~Lc~H~~ee 66 (220)
|.|..|++.| +...|..|....
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 6788887644 566777777543
No 101
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=38.59 E-value=14 Score=29.86 Aligned_cols=15 Identities=27% Similarity=0.523 Sum_probs=11.6
Q ss_pred eecCCCCCccchHHH
Q 027681 44 CFPCPFCYLEIEAHM 58 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~ 58 (220)
.-.||+|++++|-.-
T Consensus 47 ~~~cP~Cge~~~~a~ 61 (102)
T PF04475_consen 47 DTICPKCGEELDSAF 61 (102)
T ss_pred cccCCCCCCccCceE
Confidence 457999999988543
No 102
>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=38.22 E-value=19 Score=25.24 Aligned_cols=14 Identities=29% Similarity=0.771 Sum_probs=10.5
Q ss_pred CCccceecCCCCCc
Q 027681 39 DDVKACFPCPFCYL 52 (220)
Q Consensus 39 dd~r~~F~CPfC~e 52 (220)
+++..+|.||-|+.
T Consensus 29 ~~Lp~~w~CP~C~a 42 (50)
T cd00730 29 EDLPDDWVCPVCGA 42 (50)
T ss_pred hHCCCCCCCCCCCC
Confidence 35777888998864
No 103
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.14 E-value=21 Score=30.66 Aligned_cols=37 Identities=19% Similarity=0.381 Sum_probs=27.7
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccccchhHhhhh
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHF 91 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D~i~Hi 91 (220)
++..+.-.||-|+. ...+...||.|..-.-.|..+=+
T Consensus 304 ~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~ 340 (364)
T COG0675 304 PPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAAL 340 (364)
T ss_pred CCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHH
Confidence 33445578999988 33567899999998888777766
No 104
>PHA02929 N1R/p28-like protein; Provisional
Probab=37.69 E-value=6.8 Score=35.38 Aligned_cols=44 Identities=18% Similarity=0.493 Sum_probs=25.0
Q ss_pred ccceecCCCCCccchHH----------HhhhhhhcccCC---Ccccccccccccccc
Q 027681 41 VKACFPCPFCYLEIEAH----------MICSHLQEEHCF---EMKNAVCPLCAANLG 84 (220)
Q Consensus 41 ~r~~F~CPfC~ed~D~~----------~Lc~H~~eeH~~---e~k~vVCPVCa~~vg 84 (220)
...+..||.|.+++... .=|.|.--..|. -.....||+|...+.
T Consensus 171 ~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 171 RSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 34467899998765321 125553222222 124568999988654
No 105
>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=37.56 E-value=17 Score=35.55 Aligned_cols=34 Identities=32% Similarity=0.836 Sum_probs=17.0
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCccccccccccc-ccchhHhh
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA-NLGKDAAE 89 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~-~vg~D~i~ 89 (220)
+...||||+--|. | +-+.-+||||-- .||.+.++
T Consensus 379 ~~v~CP~cgA~y~------------~-~~kG~lC~vC~l~~IG~~a~G 413 (422)
T PF06957_consen 379 PSVKCPYCGAKYH------------P-EYKGQLCPVCELSEIGADASG 413 (422)
T ss_dssp -EEE-TTT--EEE------------G-GGTTSB-TTTTTBBTT---S-
T ss_pred CCeeCCCCCCccC------------h-hhCCCCCCCCcceeeCCccee
Confidence 5677999975432 1 245679999987 47777655
No 106
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=36.56 E-value=12 Score=32.85 Aligned_cols=32 Identities=19% Similarity=0.438 Sum_probs=20.7
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCC-ccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFE-MKNAV 75 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e-~k~vV 75 (220)
.|.||.|...+.+..=--+|+.-|.|| +|.|.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCCccccCce
Confidence 389999988665332223467789994 45554
No 107
>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=36.35 E-value=17 Score=29.05 Aligned_cols=38 Identities=29% Similarity=0.544 Sum_probs=22.3
Q ss_pred ecCCCCCccchH---HHhhhhhhcccCCCcccccccccccccch
Q 027681 45 FPCPFCYLEIEA---HMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 45 F~CPfC~ed~D~---~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~ 85 (220)
-.||||+....+ ..+.-|-.+++++ .=+|+-|.+.||.
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~~---~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGPY---LYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCce---eEECCCCCceeee
Confidence 369999764333 2233333232221 2689999999875
No 108
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.46 E-value=19 Score=35.02 Aligned_cols=15 Identities=40% Similarity=0.866 Sum_probs=0.0
Q ss_pred eecCCCCCccchHHH
Q 027681 44 CFPCPFCYLEIEAHM 58 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~ 58 (220)
+|+||||-.+-+...
T Consensus 374 sfKCPYCP~e~~~~~ 388 (394)
T KOG2817|consen 374 SFKCPYCPVEQLASD 388 (394)
T ss_pred eeeCCCCCcccCHHh
No 109
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=35.44 E-value=13 Score=26.09 Aligned_cols=33 Identities=27% Similarity=0.649 Sum_probs=12.2
Q ss_pred cceecCCCCCccchHHHhhhhhhcccCCCccccccccccc
Q 027681 42 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (220)
Q Consensus 42 r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~ 81 (220)
..-+||| |+..+=+- ...++.+ ..+++||-|..
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 3467887 76543211 1112222 45899999975
No 110
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.36 E-value=23 Score=36.57 Aligned_cols=30 Identities=23% Similarity=0.438 Sum_probs=25.0
Q ss_pred ccceecCCCCCc-cchHHHhhhhhhcccCCC
Q 027681 41 VKACFPCPFCYL-EIEAHMICSHLQEEHCFE 70 (220)
Q Consensus 41 ~r~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e 70 (220)
.+.--.|+||-+ -||..+|..|+..+|.++
T Consensus 179 ~rGhp~C~~C~~~fld~~el~rH~~~~h~~c 209 (669)
T KOG2231|consen 179 CRGHPLCKFCHERFLDDDELYRHLRFDHEFC 209 (669)
T ss_pred ccCCccchhhhhhhccHHHHHHhhccceehe
Confidence 344567999966 999999999999999873
No 111
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=35.34 E-value=24 Score=23.05 Aligned_cols=10 Identities=40% Similarity=1.059 Sum_probs=7.8
Q ss_pred cccccccccc
Q 027681 71 MKNAVCPLCA 80 (220)
Q Consensus 71 ~k~vVCPVCa 80 (220)
.+.++||+|.
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 5678899985
No 112
>PHA00616 hypothetical protein
Probab=34.36 E-value=21 Score=24.64 Aligned_cols=23 Identities=22% Similarity=0.320 Sum_probs=11.3
Q ss_pred ecCCCCCc-cchHHHhhhhhhccc
Q 027681 45 FPCPFCYL-EIEAHMICSHLQEEH 67 (220)
Q Consensus 45 F~CPfC~e-d~D~~~Lc~H~~eeH 67 (220)
|.||-|+. =.....|-.|+...|
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~h 25 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVH 25 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhc
Confidence 45666655 333445555554443
No 113
>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=34.29 E-value=9.2 Score=32.23 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=11.0
Q ss_pred CccceecCCCCCcc
Q 027681 40 DVKACFPCPFCYLE 53 (220)
Q Consensus 40 d~r~~F~CPfC~ed 53 (220)
|+...|.|||||-.
T Consensus 4 d~~~D~vcPwcylg 17 (209)
T cd03021 4 ELYYDVVSPYSYLA 17 (209)
T ss_pred EEEEeCCChHHHHH
Confidence 46678999999763
No 114
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=34.03 E-value=22 Score=33.94 Aligned_cols=41 Identities=22% Similarity=0.439 Sum_probs=30.1
Q ss_pred cceecCCCCCccch--HHHhhhhhhcc-cCC-----Ccccccccccccc
Q 027681 42 KACFPCPFCYLEIE--AHMICSHLQEE-HCF-----EMKNAVCPLCAAN 82 (220)
Q Consensus 42 r~~F~CPfC~ed~D--~~~Lc~H~~ee-H~~-----e~k~vVCPVCa~~ 82 (220)
..+-.||.|+.+.| +.+||.=|.-+ |+. +.+-.+|+-|-+.
T Consensus 4 ~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~ 52 (355)
T COG1499 4 ASTILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGAY 52 (355)
T ss_pred CcccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCCc
Confidence 34678999999888 88898766554 554 3345789999853
No 115
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=34.02 E-value=35 Score=24.19 Aligned_cols=33 Identities=18% Similarity=0.370 Sum_probs=15.4
Q ss_pred ccceecCCCCCc-------------cchHHHhhhhhhcccCCCcccccccc
Q 027681 41 VKACFPCPFCYL-------------EIEAHMICSHLQEEHCFEMKNAVCPL 78 (220)
Q Consensus 41 ~r~~F~CPfC~e-------------d~D~~~Lc~H~~eeH~~e~k~vVCPV 78 (220)
....+.||.... -||..++..++ -..+...||+
T Consensus 8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv 53 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPV 53 (57)
T ss_dssp SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHC-----TTTS-EE-SC
T ss_pred cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCC
Confidence 444667776643 34555555555 2345677888
No 116
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=33.74 E-value=19 Score=34.70 Aligned_cols=10 Identities=40% Similarity=1.168 Sum_probs=8.4
Q ss_pred ceecCCCCCc
Q 027681 43 ACFPCPFCYL 52 (220)
Q Consensus 43 ~~F~CPfC~e 52 (220)
.+|+||||.+
T Consensus 375 ~~FKCPYCP~ 384 (396)
T COG5109 375 LSFKCPYCPE 384 (396)
T ss_pred EEeeCCCCCc
Confidence 4799999965
No 117
>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=33.65 E-value=20 Score=33.81 Aligned_cols=38 Identities=26% Similarity=0.577 Sum_probs=23.4
Q ss_pred ecCCCCCc----cchH--------HHhhhhhhcccCCCccccccccccccc
Q 027681 45 FPCPFCYL----EIEA--------HMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 45 F~CPfC~e----d~D~--------~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
+.||.|-. +=+. ..+|..|.+.. +....+.||+|...+
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l-~~~~~~~CP~C~~~l 53 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLL-FVRGSGSCPECDTPL 53 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHH-hcCCCCCCCCCCCcc
Confidence 67999944 3332 13455666654 333457899998764
No 118
>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=33.18 E-value=12 Score=30.49 Aligned_cols=34 Identities=21% Similarity=0.192 Sum_probs=19.9
Q ss_pred hhhhhhhHHHHHHhhhcccccceeeeeee-EEEEeee
Q 027681 183 EYKLLWSQLLFKKLANKISVSSTMHFKID-VLLVIGI 218 (220)
Q Consensus 183 ~wk~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~ 218 (220)
.++....+. .+.|.+..|..|-.|-|+ -.++.|.
T Consensus 156 ~~~~~~~~~--~~~a~~~gv~G~Pt~vv~g~~~~~G~ 190 (201)
T cd03024 156 EYADEVRAD--EARARQLGISGVPFFVFNGKYAVSGA 190 (201)
T ss_pred ccchHHHHH--HHHHHHCCCCcCCEEEECCeEeecCC
Confidence 344444443 245667788888888887 4445553
No 119
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=32.50 E-value=11 Score=29.39 Aligned_cols=38 Identities=24% Similarity=0.563 Sum_probs=12.7
Q ss_pred cCCCCCccchHHHhh-hhhhcccCC-----------Cccccccccccccc
Q 027681 46 PCPFCYLEIEAHMIC-SHLQEEHCF-----------EMKNAVCPLCAANL 83 (220)
Q Consensus 46 ~CPfC~ed~D~~~Lc-~H~~eeH~~-----------e~k~vVCPVCa~~v 83 (220)
.||+|.+.++...+- .=|..-|.+ +++.-+|++|..+.
T Consensus 16 ~C~~C~~~i~~~~~~~~~C~~GH~w~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 16 KCPICGAPIPFDDLDEAQCENGHVWPRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp -------------SSEEE-TTS-EEEB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred cccccccccccCCcCEeECCCCCEEeeeeeeeeeeccCCeeEcCCCCCEE
Confidence 499998877655543 447777766 56668899998874
No 120
>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=30.93 E-value=12 Score=30.14 Aligned_cols=36 Identities=17% Similarity=0.031 Sum_probs=21.0
Q ss_pred ChhhhhhhhhHHHHHHhhhcccccceeeeeeeEEEEee
Q 027681 180 PSSEYKLLWSQLLFKKLANKISVSSTMHFKIDVLLVIG 217 (220)
Q Consensus 180 ~~~~wk~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (220)
.+..++..-.+.. +.|.+..|.++-.|-|+--.++|
T Consensus 145 ~~~~~~~~l~~~~--~~a~~~gi~gvPtfvv~g~~~~G 180 (192)
T cd03022 145 DDPAVKAALRANT--EEAIARGVFGVPTFVVDGEMFWG 180 (192)
T ss_pred CCHHHHHHHHHHH--HHHHHcCCCcCCeEEECCeeecc
Confidence 3444554444443 34566777888777776555555
No 121
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.56 E-value=27 Score=38.03 Aligned_cols=38 Identities=24% Similarity=0.481 Sum_probs=22.3
Q ss_pred ceecCCCCCccchHHHhhhhhhcccCCCcccccccccccccc
Q 027681 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 84 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg 84 (220)
..|.||.|+..-...--|..|.. ......||-|-..+.
T Consensus 637 ~~frCP~CG~~Te~i~fCP~CG~----~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRCGI----EVEEDECEKCGREPT 674 (1121)
T ss_pred CcccCCCCCCCCCcceeCccccC----cCCCCcCCCCCCCCC
Confidence 45677777665444555666522 233356888887743
No 122
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=30.50 E-value=25 Score=34.03 Aligned_cols=41 Identities=20% Similarity=0.386 Sum_probs=30.4
Q ss_pred ceecCCC--CCc-cchHHHhhhhhhcccCC-----------------Cccccccccccccc
Q 027681 43 ACFPCPF--CYL-EIEAHMICSHLQEEHCF-----------------EMKNAVCPLCAANL 83 (220)
Q Consensus 43 ~~F~CPf--C~e-d~D~~~Lc~H~~eeH~~-----------------e~k~vVCPVCa~~v 83 (220)
--|+||. |.+ .-.+-||--|...-|+. +.|+-+|+||.++.
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhh
Confidence 3588985 765 56778888888888832 34677899999984
No 123
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.05 E-value=7.9 Score=31.39 Aligned_cols=40 Identities=23% Similarity=0.688 Sum_probs=23.1
Q ss_pred ccceecCCCCCccchHH-Hh-hhhhhcccCCCc---ccccccccc
Q 027681 41 VKACFPCPFCYLEIEAH-MI-CSHLQEEHCFEM---KNAVCPLCA 80 (220)
Q Consensus 41 ~r~~F~CPfC~ed~D~~-~L-c~H~~eeH~~e~---k~vVCPVCa 80 (220)
...++.||.|.+.|... .| |-|---..+... ....||+|.
T Consensus 10 ~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccccChhhHHHhhcCccccccchHhHHHHHHhcCCCcCCcccC
Confidence 33578899997766665 22 223222222222 337899999
No 124
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=30.00 E-value=29 Score=25.26 Aligned_cols=47 Identities=17% Similarity=0.293 Sum_probs=21.6
Q ss_pred CCccceecCC--CCCccchHHHhhhhhhcccC----CCcccccccccccccch
Q 027681 39 DDVKACFPCP--FCYLEIEAHMICSHLQEEHC----FEMKNAVCPLCAANLGK 85 (220)
Q Consensus 39 dd~r~~F~CP--fC~ed~D~~~Lc~H~~eeH~----~e~k~vVCPVCa~~vg~ 85 (220)
++-.+...|| -|..-|=..=|...+..... +....|.||.|...+.-
T Consensus 15 ~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 15 DGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp T-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 3344577887 88888877778777765433 44566779999988654
No 125
>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=29.83 E-value=26 Score=34.79 Aligned_cols=29 Identities=24% Similarity=0.615 Sum_probs=23.5
Q ss_pred cccccccccccc--chhHhhhhhhhccchhh
Q 027681 72 KNAVCPLCAANL--GKDAAEHFMVQHASSLK 100 (220)
Q Consensus 72 k~vVCPVCa~~v--g~D~i~Hit~QH~~~fK 100 (220)
+.-+||+|..+- ..++..|+..+|...++
T Consensus 56 rFWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 56 RFWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eEeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 345699999773 55899999999998775
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=29.55 E-value=38 Score=24.24 Aligned_cols=37 Identities=22% Similarity=0.534 Sum_probs=22.1
Q ss_pred eecCCCCCccchHHHhhhhhh------------------cccCCCccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQ------------------EEHCFEMKNAVCPLCAA 81 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~------------------eeH~~e~k~vVCPVCa~ 81 (220)
--.||+|-..+|-..|+.=.. +.|.. ....+||.|..
T Consensus 7 iL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~-eg~L~Cp~c~r 61 (68)
T PF03966_consen 7 ILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIV-EGELICPECGR 61 (68)
T ss_dssp TBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETT-TTEEEETTTTE
T ss_pred hhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhccccc-CCEEEcCCCCC
Confidence 457999966787666665221 12333 35678999964
No 127
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.41 E-value=16 Score=26.33 Aligned_cols=10 Identities=40% Similarity=0.916 Sum_probs=6.3
Q ss_pred cceecCCCCC
Q 027681 42 KACFPCPFCY 51 (220)
Q Consensus 42 r~~F~CPfC~ 51 (220)
+..|.||.|+
T Consensus 12 ~v~~~Cp~cG 21 (55)
T PF13824_consen 12 HVNFECPDCG 21 (55)
T ss_pred ccCCcCCCCC
Confidence 4566777774
No 128
>PRK12860 transcriptional activator FlhC; Provisional
Probab=29.15 E-value=42 Score=29.60 Aligned_cols=32 Identities=25% Similarity=0.491 Sum_probs=20.7
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCc-ccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEM-KNAVCPLCA 80 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~-k~vVCPVCa 80 (220)
-++-..-+|..|+-.|= . |..|. .+-+||+|.
T Consensus 129 s~~L~l~~C~~Cgg~fv-----~-----~~~e~~~~f~CplC~ 161 (189)
T PRK12860 129 AGMLQLARCCRCGGKFV-----T-----HAHDLRHNFVCGLCQ 161 (189)
T ss_pred CCCeeeccCCCCCCCee-----c-----cccccCCCCcCCCCC
Confidence 34566788999965441 1 23343 457999997
No 129
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=29.06 E-value=36 Score=31.84 Aligned_cols=52 Identities=19% Similarity=0.408 Sum_probs=38.3
Q ss_pred eecCCCCCccchHHHhh-hhhhcccCCCcccccccccccccch--hHhhhhhhhccc
Q 027681 44 CFPCPFCYLEIEAHMIC-SHLQEEHCFEMKNAVCPLCAANLGK--DAAEHFMVQHAS 97 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc-~H~~eeH~~e~k~vVCPVCa~~vg~--D~i~Hit~QH~~ 97 (220)
-+.|++|++-|+..=|. -|+.. |.-| |+-.||.|..--.. |+-.||.+.-..
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRT-HTGE-KPF~C~hC~kAFADRSNLRAHmQTHS~~ 241 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRT-HTGE-KPFSCPHCGKAFADRSNLRAHMQTHSDV 241 (279)
T ss_pred CcccccccccccchHHhhccccc-ccCC-CCccCCcccchhcchHHHHHHHHhhcCC
Confidence 57899999999976554 46655 6553 67799999988644 999999654443
No 130
>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=27.09 E-value=24 Score=27.09 Aligned_cols=18 Identities=28% Similarity=0.493 Sum_probs=10.3
Q ss_pred CCccceecCCCCCccchH
Q 027681 39 DDVKACFPCPFCYLEIEA 56 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~ 56 (220)
=|+-+.|.||-|++.+++
T Consensus 60 VENMs~~~Cp~Cg~~~~i 77 (81)
T PF10609_consen 60 VENMSYFVCPHCGERIYI 77 (81)
T ss_dssp EECT-EEE-TTT--EEET
T ss_pred EECCCccCCCCCCCeecC
Confidence 456789999999886553
No 131
>PF14968 CCDC84: Coiled coil protein 84
Probab=26.95 E-value=32 Score=32.72 Aligned_cols=20 Identities=35% Similarity=0.732 Sum_probs=15.2
Q ss_pred CCCccceecCCCCCccchHH
Q 027681 38 DDDVKACFPCPFCYLEIEAH 57 (220)
Q Consensus 38 ddd~r~~F~CPfC~ed~D~~ 57 (220)
|.+-+..|=|+||+.+++..
T Consensus 52 ~~~~~~~fWC~fC~~ev~~~ 71 (336)
T PF14968_consen 52 DPEHRNRFWCVFCDCEVREH 71 (336)
T ss_pred CccccceeEeeCccchhhhc
Confidence 34567789999998877654
No 132
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.54 E-value=33 Score=32.99 Aligned_cols=22 Identities=32% Similarity=0.863 Sum_probs=18.6
Q ss_pred eecCCCCCccchHHHhhhhhhc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQE 65 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~e 65 (220)
+.-||||.-.+...+.|.|++.
T Consensus 2 e~iCP~CkLsv~~~~m~~Hiea 23 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIEA 23 (393)
T ss_pred cccccceecccCHHHHHHHHHh
Confidence 4569999878888999999983
No 133
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=26.54 E-value=49 Score=22.64 Aligned_cols=39 Identities=26% Similarity=0.493 Sum_probs=23.3
Q ss_pred CccccCCCccceecCCCCCccchHHHhhhhhhcccCCCccccccccc
Q 027681 33 DETEIDDDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLC 79 (220)
Q Consensus 33 de~e~ddd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVC 79 (220)
+++-.....+..+.||.|+-++...-= . +. .+..-||.|
T Consensus 17 ~~v~~~s~~~v~W~C~~Cgh~w~~~v~-~------R~-~~~~~CP~C 55 (55)
T PF14311_consen 17 SEVTPGSNKKVWWKCPKCGHEWKASVN-D------RT-RRGKGCPYC 55 (55)
T ss_pred HHhCcCCCCEEEEECCCCCCeeEccHh-h------hc-cCCCCCCCC
Confidence 344444456778999999765543211 1 11 456789988
No 134
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=26.52 E-value=17 Score=24.87 Aligned_cols=10 Identities=50% Similarity=1.195 Sum_probs=7.9
Q ss_pred ceecCCCCCc
Q 027681 43 ACFPCPFCYL 52 (220)
Q Consensus 43 ~~F~CPfC~e 52 (220)
..+.||+|+.
T Consensus 5 ~d~~Cp~C~~ 14 (98)
T cd02972 5 FDPLCPYCYL 14 (98)
T ss_pred ECCCCHhHHh
Confidence 3678999976
No 135
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=26.43 E-value=32 Score=33.97 Aligned_cols=19 Identities=32% Similarity=0.593 Sum_probs=14.6
Q ss_pred cCCCcccccccccccccch
Q 027681 67 HCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 67 H~~e~k~vVCPVCa~~vg~ 85 (220)
.-.+++.-|||||...+|.
T Consensus 31 ~~~~PNt~vcpv~lg~PG~ 49 (474)
T PRK05477 31 FGAEPNTNVCPVCLGLPGA 49 (474)
T ss_pred cCCCCCCCcCccccCCCCC
Confidence 3346788999999999654
No 136
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.11 E-value=22 Score=33.46 Aligned_cols=40 Identities=30% Similarity=0.653 Sum_probs=24.5
Q ss_pred eecCCCCCc--cchHHHh-hhhhhcccCCCccc-----cccccccccc
Q 027681 44 CFPCPFCYL--EIEAHMI-CSHLQEEHCFEMKN-----AVCPLCAANL 83 (220)
Q Consensus 44 ~F~CPfC~e--d~D~~~L-c~H~~eeH~~e~k~-----vVCPVCa~~v 83 (220)
+-.||+|++ -+--+.. |.|+-=.-|.-++- ..||-|.+.+
T Consensus 239 ~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 239 DTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred CceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 567999987 3444444 77744333333322 4799998875
No 137
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=26.11 E-value=49 Score=28.80 Aligned_cols=31 Identities=26% Similarity=0.699 Sum_probs=22.5
Q ss_pred ccceecCCCCCc--cchHHHhhhhhhcccCCCccccccccccccc
Q 027681 41 VKACFPCPFCYL--EIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (220)
Q Consensus 41 ~r~~F~CPfC~e--d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~v 83 (220)
....|.||-|.. .||.+-+.. -.||.|.+.+
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 345799999965 666554433 5999999985
No 138
>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=25.83 E-value=34 Score=24.24 Aligned_cols=9 Identities=33% Similarity=1.195 Sum_probs=7.9
Q ss_pred eecCCCCCc
Q 027681 44 CFPCPFCYL 52 (220)
Q Consensus 44 ~F~CPfC~e 52 (220)
.|.||+|+.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 899999974
No 139
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=25.47 E-value=44 Score=30.89 Aligned_cols=29 Identities=24% Similarity=0.532 Sum_probs=20.5
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
--+||-|.+-+-...|-.. ..|||-|...
T Consensus 27 ~~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEAN----------LNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHhc----------CCCCCCCCCC
Confidence 3569999886666555332 3599999886
No 140
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=25.25 E-value=24 Score=27.36 Aligned_cols=8 Identities=50% Similarity=1.364 Sum_probs=6.1
Q ss_pred ecCCCCCc
Q 027681 45 FPCPFCYL 52 (220)
Q Consensus 45 F~CPfC~e 52 (220)
.+||+|++
T Consensus 2 I~CP~CG~ 9 (84)
T PF04267_consen 2 IPCPHCGP 9 (84)
T ss_dssp EEETTTEE
T ss_pred ccCCCCCc
Confidence 47888876
No 141
>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=24.84 E-value=34 Score=27.38 Aligned_cols=34 Identities=21% Similarity=0.516 Sum_probs=23.5
Q ss_pred CccceecCCCCCc-cchHHHhhhhhhcccCCCcccccccccccccchh
Q 027681 40 DVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKD 86 (220)
Q Consensus 40 d~r~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~vg~D 86 (220)
|+.....||-|+. =||+. -.++|||-|..-.-..
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 4556678999975 55666 2467899998875544
No 142
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=24.83 E-value=18 Score=28.62 Aligned_cols=18 Identities=39% Similarity=0.761 Sum_probs=13.7
Q ss_pred ccCCCccceecCCCCCcc
Q 027681 36 EIDDDVKACFPCPFCYLE 53 (220)
Q Consensus 36 e~ddd~r~~F~CPfC~ed 53 (220)
|.|..+++.+.||+|+..
T Consensus 27 ~ie~~~~~~~~Cp~C~~~ 44 (89)
T COG1997 27 EIEAQQRAKHVCPFCGRT 44 (89)
T ss_pred HHHHHHhcCCcCCCCCCc
Confidence 345567889999999764
No 143
>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=24.82 E-value=48 Score=30.61 Aligned_cols=29 Identities=24% Similarity=0.514 Sum_probs=20.5
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
-..||-|++-+-...|-. +..|||-|...
T Consensus 26 ~~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELER----------NLEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHh----------hCCCCCCCCCc
Confidence 345999988666555443 24699999875
No 144
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.63 E-value=33 Score=27.41 Aligned_cols=32 Identities=22% Similarity=0.461 Sum_probs=21.4
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
++.+..+.|+-|+..+..... ....||-|...
T Consensus 66 e~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 66 VDEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred EecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 356778999999866554321 22359999875
No 145
>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=24.31 E-value=13 Score=28.84 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=15.5
Q ss_pred ceecCCCCCc-cchHHHhhhhh
Q 027681 43 ACFPCPFCYL-EIEAHMICSHL 63 (220)
Q Consensus 43 ~~F~CPfC~e-d~D~~~Lc~H~ 63 (220)
..|.||+|.. .-.+..|..+.
T Consensus 20 ~d~~Cp~C~~~~~~~~~~~~~~ 41 (162)
T PF13462_consen 20 FDFQCPHCAKFHEELEKLLKKY 41 (162)
T ss_dssp E-TTSHHHHHHHHHHHHHHHHH
T ss_pred ECCCCHhHHHHHHHHhhhhhhc
Confidence 4799999965 66666888875
No 146
>PF14353 CpXC: CpXC protein
Probab=24.16 E-value=38 Score=26.65 Aligned_cols=15 Identities=27% Similarity=0.636 Sum_probs=11.6
Q ss_pred ceecCCCCCccchHH
Q 027681 43 ACFPCPFCYLEIEAH 57 (220)
Q Consensus 43 ~~F~CPfC~ed~D~~ 57 (220)
..|.||.|+..+-+.
T Consensus 37 ~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLE 51 (128)
T ss_pred CEEECCCCCCceecC
Confidence 479999999866553
No 147
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=24.15 E-value=25 Score=33.30 Aligned_cols=40 Identities=23% Similarity=0.434 Sum_probs=24.5
Q ss_pred eecCCCCCccchHHHhhhhhhccc-CCCccccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEH-CFEMKNAVCPLCAANL 83 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH-~~e~k~vVCPVCa~~v 83 (220)
+-.||+|+-+---...|++|-... |.|..+.+|.+|...+
T Consensus 136 ~g~CP~C~~~~a~g~~Ce~cG~~~~~~~l~~p~~~~~g~~~ 176 (391)
T PF09334_consen 136 EGTCPYCGSDKARGDQCENCGRPLEPEELINPVCKICGSPP 176 (391)
T ss_dssp TCEETTT--SSCTTTEETTTSSBEECCCSECEEETTTS-B-
T ss_pred eccccCcCccccCCCcccCCCCCcccccccCCccccccccC
Confidence 356999974444445666665432 5677889999998874
No 148
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=24.13 E-value=35 Score=29.80 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=11.0
Q ss_pred ecCCCCCccchHHH
Q 027681 45 FPCPFCYLEIEAHM 58 (220)
Q Consensus 45 F~CPfC~ed~D~~~ 58 (220)
=+||+|++-+|-.+
T Consensus 155 P~CPlCg~PlDP~G 168 (171)
T PF11290_consen 155 PPCPLCGEPLDPEG 168 (171)
T ss_pred CCCCCCCCCCCCCC
Confidence 47999999888554
No 149
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.08 E-value=21 Score=34.61 Aligned_cols=47 Identities=23% Similarity=0.497 Sum_probs=27.1
Q ss_pred CCccceecCCCCCccchHH--HhhhhhhcccCCC---cccccccccccccch
Q 027681 39 DDVKACFPCPFCYLEIEAH--MICSHLQEEHCFE---MKNAVCPLCAANLGK 85 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~--~Lc~H~~eeH~~e---~k~vVCPVCa~~vg~ 85 (220)
++++..+.||.|.+.|... .=|.|.-=..|.. .....||+|...++.
T Consensus 21 ~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred cccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 4566789999997755443 2244422111111 123589999987543
No 150
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.08 E-value=23 Score=31.88 Aligned_cols=47 Identities=17% Similarity=0.036 Sum_probs=29.5
Q ss_pred cccccccCCCChhhhhhhhhHHHHHHhhhcccccceeeeee-eEEEEeee
Q 027681 170 SLASDLKRYPPSSEYKLLWSQLLFKKLANKISVSSTMHFKI-DVLLVIGI 218 (220)
Q Consensus 170 ~~~~~~kr~~~~~~wk~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~ 218 (220)
..-...++...+..|+...-+-. +-|..+.|...--|-| +-+.|-|.
T Consensus 152 LD~~~~~~~L~s~~~~~avr~d~--~~A~e~gI~gVP~fv~d~~~~V~Ga 199 (225)
T COG2761 152 LDREEFKADLASDAAKDAVRQDE--AAAQEMGIRGVPTFVFDGKYAVSGA 199 (225)
T ss_pred CCHHHHHHHHhChHHHHHHHHHH--HHHHHCCCccCceEEEcCcEeecCC
Confidence 33444667777777777665554 3566777777666766 55555554
No 151
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.00 E-value=34 Score=31.24 Aligned_cols=54 Identities=22% Similarity=0.485 Sum_probs=33.9
Q ss_pred ceecCCC--CCccchHHHhhhhhhcccCCCcccccccccccc-c-chhHhhhhhhhccchhh
Q 027681 43 ACFPCPF--CYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN-L-GKDAAEHFMVQHASSLK 100 (220)
Q Consensus 43 ~~F~CPf--C~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~-v-g~D~i~Hit~QH~~~fK 100 (220)
..|.||- |.+-+|--. |- |.|.......+|-+|... + +.=+-.||+-+|-++|.
T Consensus 78 ~~~~cqvagc~~~~d~lD---~~-E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~Fq 135 (253)
T KOG4173|consen 78 PAFACQVAGCCQVFDALD---DY-EHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSLFQ 135 (253)
T ss_pred ccccccccchHHHHhhhh---hH-HHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHHHH
Confidence 4789985 333333221 11 124444455799999987 3 33455799999999883
No 152
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=23.72 E-value=50 Score=30.89 Aligned_cols=29 Identities=24% Similarity=0.479 Sum_probs=20.8
Q ss_pred eecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
-.+||-|.+-+-...|-. +..|||-|...
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 356999988766665543 34699999875
No 153
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=23.62 E-value=47 Score=26.92 Aligned_cols=24 Identities=21% Similarity=0.527 Sum_probs=15.5
Q ss_pred ccccccccccc-----chhHhhhhhhhcc
Q 027681 73 NAVCPLCAANL-----GKDAAEHFMVQHA 96 (220)
Q Consensus 73 ~vVCPVCa~~v-----g~D~i~Hit~QH~ 96 (220)
.|.||+|.... ......|++.-||
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HG 53 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHG 53 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhccc
Confidence 78888888542 3346677755555
No 154
>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=23.06 E-value=11 Score=23.66 Aligned_cols=8 Identities=50% Similarity=1.364 Sum_probs=3.9
Q ss_pred cccccccc
Q 027681 72 KNAVCPLC 79 (220)
Q Consensus 72 k~vVCPVC 79 (220)
....||+|
T Consensus 34 ~~~~CP~C 41 (41)
T PF00097_consen 34 GSVKCPLC 41 (41)
T ss_dssp SSSBTTTT
T ss_pred CCccCCcC
Confidence 33445555
No 155
>PF14828 Amnionless: Amnionless
Probab=22.95 E-value=54 Score=31.97 Aligned_cols=42 Identities=29% Similarity=0.626 Sum_probs=27.0
Q ss_pred ecCCCCCccchHHHhhhhh----hcccCCCccc---ccccccccccchhH
Q 027681 45 FPCPFCYLEIEAHMICSHL----QEEHCFEMKN---AVCPLCAANLGKDA 87 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~----~eeH~~e~k~---vVCPVCa~~vg~D~ 87 (220)
-.|+ |+.+.-+..+|..+ ..-||.++=. --||||-++++...
T Consensus 192 ~gC~-C~n~~~l~~ICs~v~~~C~~~~C~~pl~P~GhCC~iCGa~v~~~~ 240 (437)
T PF14828_consen 192 SGCP-CGNDEVLEWICSNVLQRCPKPHCRSPLRPEGHCCPICGAIVTLEY 240 (437)
T ss_pred ccCc-cCcccchhhhhHHhhCcCCCCccCCCCCCCCCchhhcceEEEEee
Confidence 3466 77776677777654 4455554432 45999999975533
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=22.86 E-value=31 Score=27.26 Aligned_cols=18 Identities=28% Similarity=0.410 Sum_probs=12.4
Q ss_pred HhhhcccccceeeeeeeE
Q 027681 195 KLANKISVSSTMHFKIDV 212 (220)
Q Consensus 195 ~~~~~~~~~~~~~~~~~~ 212 (220)
+++++..|.+|--|-|+-
T Consensus 134 ~~~~~~gi~gTPt~iInG 151 (178)
T cd03019 134 KLAKKYKITGVPAFVVNG 151 (178)
T ss_pred HHHHHcCCCCCCeEEECC
Confidence 456677777777777754
No 157
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=22.66 E-value=31 Score=27.40 Aligned_cols=32 Identities=19% Similarity=0.409 Sum_probs=20.6
Q ss_pred CCccceecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 39 dd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+..+..+.|+-|+..|..... ....||.|...
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 96 (114)
T PRK03681 65 EEQEAECWCETCQQYVTLLTQ------------RVRRCPQCHGD 96 (114)
T ss_pred EeeCcEEEcccCCCeeecCCc------------cCCcCcCcCCC
Confidence 456778999999864433211 11469999864
No 158
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.36 E-value=41 Score=34.44 Aligned_cols=39 Identities=15% Similarity=0.377 Sum_probs=25.8
Q ss_pred CccceecCCCCCccchH----HHh-hhhhhcccCCCcccccccccccc
Q 027681 40 DVKACFPCPFCYLEIEA----HMI-CSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 40 d~r~~F~CPfC~ed~D~----~~L-c~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
+....+.||.|+-.+.. ..| |.||.-. ...-.||-|...
T Consensus 388 ~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~----~~p~~Cp~Cgs~ 431 (665)
T PRK14873 388 RCRTPARCRHCTGPLGLPSAGGTPRCRWCGRA----APDWRCPRCGSD 431 (665)
T ss_pred hCcCeeECCCCCCceeEecCCCeeECCCCcCC----CcCccCCCCcCC
Confidence 45668999999754433 235 6666642 236699999886
No 159
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.33 E-value=41 Score=35.05 Aligned_cols=40 Identities=23% Similarity=0.423 Sum_probs=27.0
Q ss_pred CccceecCCCCCccc----hHHHhhhh-hhcccCCCcccccccccccc
Q 027681 40 DVKACFPCPFCYLEI----EAHMICSH-LQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 40 d~r~~F~CPfC~ed~----D~~~Lc~H-~~eeH~~e~k~vVCPVCa~~ 82 (220)
+....+.||.|+-.+ +...|.|| |.- + +..+-.||-|...
T Consensus 440 ~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~-~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 440 DCGYIAECPNCDSPLTLHKATGQLRCHYCGY-Q--EPIPQSCPECGSE 484 (730)
T ss_pred cCCCcccCCCCCcceEEecCCCeeEeCCCCC-C--CCCCCCCCCCCCC
Confidence 455679999996533 33455555 332 2 5677899999987
No 160
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=22.12 E-value=31 Score=23.26 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=7.8
Q ss_pred eecCCCCCcc
Q 027681 44 CFPCPFCYLE 53 (220)
Q Consensus 44 ~F~CPfC~ed 53 (220)
.-.||||+.-
T Consensus 29 ~~~CpYCg~~ 38 (40)
T PF10276_consen 29 PVVCPYCGTR 38 (40)
T ss_dssp EEEETTTTEE
T ss_pred eEECCCCCCE
Confidence 5779999753
No 161
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=21.91 E-value=57 Score=32.09 Aligned_cols=67 Identities=25% Similarity=0.483 Sum_probs=0.0
Q ss_pred hchhhhhhhhhcCCCCCCccCccccCCCccceecCCCCCc-cchHHHhhhhhhcccCCCcccccccccccc--cchhHhh
Q 027681 13 AKHFSAVRASRLNTDNHSIVDETEIDDDVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN--LGKDAAE 89 (220)
Q Consensus 13 akr~~a~q~~r~~sd~~~~~de~e~ddd~r~~F~CPfC~e-d~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~--vg~D~i~ 89 (220)
.|||-...+-+.+.-++++ .|+||.|+- ==-.++|..|+.-.|.- .|.--|--|..+ --.|+..
T Consensus 244 ~KrFaTeklL~~Hv~rHvn------------~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~c~~esdL~k 310 (467)
T KOG3608|consen 244 FKRFATEKLLKSHVVRHVN------------CYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTRCVRESDLAK 310 (467)
T ss_pred HHHHhHHHHHHHHHHHhhh------------cccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhhhccHHHHHH
Q ss_pred hhhhh
Q 027681 90 HFMVQ 94 (220)
Q Consensus 90 Hit~Q 94 (220)
|+ |
T Consensus 311 H~--~ 313 (467)
T KOG3608|consen 311 HV--Q 313 (467)
T ss_pred HH--H
No 162
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=21.70 E-value=36 Score=32.17 Aligned_cols=19 Identities=16% Similarity=0.427 Sum_probs=14.3
Q ss_pred ccccccccccccchhHhhh
Q 027681 72 KNAVCPLCAANLGKDAAEH 90 (220)
Q Consensus 72 k~vVCPVCa~~vg~D~i~H 90 (220)
+..+||||..++...||.-
T Consensus 184 ~~~~CPvCGS~PvaSmV~~ 202 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQI 202 (308)
T ss_pred ccccCCCcCCCCcceeeee
Confidence 4479999999977666643
No 163
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=21.58 E-value=67 Score=20.70 Aligned_cols=31 Identities=19% Similarity=0.378 Sum_probs=17.1
Q ss_pred ecCCCCCccchHHHhhhhhhcccCCCccccccccccc
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~ 81 (220)
..||-|...|++..=- =+...+.+-||.|..
T Consensus 3 i~CP~C~~~f~v~~~~------l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK------LPAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCHHH------cccCCcEEECCCCCc
Confidence 4688886655443211 122355677888764
No 164
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.57 E-value=48 Score=35.33 Aligned_cols=36 Identities=19% Similarity=0.405 Sum_probs=24.0
Q ss_pred cceecCCCCCccchHHHhhhhhhcccCCCcccccccccccc
Q 027681 42 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 42 r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
-..+.||.|+..|....-- .-.|.+..+.||.|.-.
T Consensus 248 s~~~~c~~~g~~~~~~~~~-----~FSfNsp~G~Cp~C~G~ 283 (924)
T TIGR00630 248 SKHAACPECGFSLPELEPR-----LFSFNSPYGACPECSGL 283 (924)
T ss_pred hhcccCcccCcccCcCChh-----hcCCCCCcCCCCCCccc
Confidence 3569999998766532211 13566677999999654
No 165
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=21.56 E-value=27 Score=27.62 Aligned_cols=14 Identities=29% Similarity=0.603 Sum_probs=11.3
Q ss_pred CCccceecCCCCCc
Q 027681 39 DDVKACFPCPFCYL 52 (220)
Q Consensus 39 dd~r~~F~CPfC~e 52 (220)
.-..+.|.|+||+.
T Consensus 31 i~Qhaky~CsfCGK 44 (92)
T KOG0402|consen 31 IQQHAKYTCSFCGK 44 (92)
T ss_pred HHHhhhhhhhhcch
Confidence 44677899999987
No 166
>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=21.53 E-value=64 Score=19.40 Aligned_cols=20 Identities=25% Similarity=0.644 Sum_probs=10.3
Q ss_pred ecCCCCCccch-HHHhhhhhh
Q 027681 45 FPCPFCYLEIE-AHMICSHLQ 64 (220)
Q Consensus 45 F~CPfC~ed~D-~~~Lc~H~~ 64 (220)
|.|..|...|. ...+-.|+.
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred eEccccCCccCCHHHHHHHHC
Confidence 55666655443 444455543
No 167
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.39 E-value=48 Score=36.89 Aligned_cols=21 Identities=24% Similarity=0.350 Sum_probs=11.4
Q ss_pred eecCCCCCccchHHHhhhhhhc
Q 027681 44 CFPCPFCYLEIEAHMICSHLQE 65 (220)
Q Consensus 44 ~F~CPfC~ed~D~~~Lc~H~~e 65 (220)
.+.||-|+...- ...|..|-.
T Consensus 667 ~rkCPkCG~~t~-~~fCP~CGs 687 (1337)
T PRK14714 667 RRRCPSCGTETY-ENRCPDCGT 687 (1337)
T ss_pred EEECCCCCCccc-cccCcccCC
Confidence 577777765321 235555554
No 168
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=21.25 E-value=42 Score=26.09 Aligned_cols=14 Identities=29% Similarity=0.821 Sum_probs=8.1
Q ss_pred ecCCCCCccchHHHh
Q 027681 45 FPCPFCYLEIEAHMI 59 (220)
Q Consensus 45 F~CPfC~ed~D~~~L 59 (220)
.+||+|++ =|..++
T Consensus 2 I~CP~CG~-R~~~EF 15 (84)
T TIGR01374 2 IPCPYCGP-RPEEEF 15 (84)
T ss_pred ccCCCCCC-ccHhhE
Confidence 46888873 344333
No 169
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=21.23 E-value=46 Score=33.62 Aligned_cols=23 Identities=26% Similarity=0.437 Sum_probs=17.2
Q ss_pred hhcccCCCcccccccccccccch
Q 027681 63 LQEEHCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 63 ~~eeH~~e~k~vVCPVCa~~vg~ 85 (220)
|..+.-.+++.-|||||...+|.
T Consensus 83 c~~~~g~~PNt~vcpvclg~PGt 105 (544)
T PLN02751 83 CPYNYGAEPNTTVCPVCMGLPGT 105 (544)
T ss_pred CCcccCCCCccCcCccccCCCCC
Confidence 33445557889999999999654
No 170
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The presence of motifs with seven invariant Cys residues in the N-terminal 50 residues, including three instances of CXXC, would be consistent with function as an oxidoreductase with FeS clusters. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon.
Probab=21.22 E-value=40 Score=32.44 Aligned_cols=33 Identities=18% Similarity=0.527 Sum_probs=20.9
Q ss_pred eecCCCCCc--cchHHHh-hhhhhcccCCCcccccccccccc
Q 027681 44 CFPCPFCYL--EIEAHMI-CSHLQEEHCFEMKNAVCPLCAAN 82 (220)
Q Consensus 44 ~F~CPfC~e--d~D~~~L-c~H~~eeH~~e~k~vVCPVCa~~ 82 (220)
-..||||+. --+...| |.||.. -+..||-|...
T Consensus 10 ~~~C~wC~~p~~~~~~~~~c~~C~~------~~~~C~yC~~~ 45 (404)
T TIGR03278 10 RGFCRYCYFKKVDDEQPFGCKNCPP------GTKGCDYCTRS 45 (404)
T ss_pred CCcCCCCCCCCCCCCCCCCCCcCCC------CCCCCCCCCch
Confidence 457999975 3334445 555532 35689999665
No 171
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.17 E-value=27 Score=33.40 Aligned_cols=47 Identities=23% Similarity=0.488 Sum_probs=32.3
Q ss_pred ccCCCccceecCCCCCccchHHHhhhhhhcccCCCc---------cccccccccccc
Q 027681 36 EIDDDVKACFPCPFCYLEIEAHMICSHLQEEHCFEM---------KNAVCPLCAANL 83 (220)
Q Consensus 36 e~ddd~r~~F~CPfC~ed~D~~~Lc~H~~eeH~~e~---------k~vVCPVCa~~v 83 (220)
.++++... +.|--|-|+|...+.+.++-=.|.|-. ..-.||||-..+
T Consensus 222 ~~~~~~~~-~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 222 KGDDEDAT-DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred cccccCCC-ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 44444444 899999998888777666666666622 335799998754
No 172
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=20.99 E-value=14 Score=29.66 Aligned_cols=19 Identities=32% Similarity=0.670 Sum_probs=12.0
Q ss_pred cceecCCCCCc-cchHHHhh
Q 027681 42 KACFPCPFCYL-EIEAHMIC 60 (220)
Q Consensus 42 r~~F~CPfC~e-d~D~~~Lc 60 (220)
-.+|.||||+- .--+..|.
T Consensus 5 ~~D~~Cp~cy~~~~~l~~l~ 24 (193)
T PF01323_consen 5 FFDFICPWCYLASPRLRKLR 24 (193)
T ss_dssp EEBTTBHHHHHHHHHHHHHH
T ss_pred EEeCCCHHHHHHHHHHHHHH
Confidence 45789999975 33344444
No 173
>PF14279 HNH_5: HNH endonuclease
Probab=20.57 E-value=42 Score=24.90 Aligned_cols=40 Identities=28% Similarity=0.659 Sum_probs=26.4
Q ss_pred CCCCCccchHHHhhhhhhcccCC--------CcccccccccccccchhHhhhh
Q 027681 47 CPFCYLEIEAHMICSHLQEEHCF--------EMKNAVCPLCAANLGKDAAEHF 91 (220)
Q Consensus 47 CPfC~ed~D~~~Lc~H~~eeH~~--------e~k~vVCPVCa~~vg~D~i~Hi 91 (220)
|.||.++++....- +||=. ..+. ||-.|-..+|..+-+++
T Consensus 1 Ci~C~~~~~~~~~s----~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~~l 48 (71)
T PF14279_consen 1 CIYCNKEKSESNFS----EEHIIPESLGGKLKINN-VCDKCNNKFGSKVDAEL 48 (71)
T ss_pred CccCCCCCCccCCC----ccccCchhcCCcccccc-hhHHHhHHHhHHHHHHH
Confidence 89998876554321 44533 3455 99999999887555555
No 174
>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=20.56 E-value=56 Score=28.70 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=8.4
Q ss_pred ccccccccccc
Q 027681 72 KNAVCPLCAAN 82 (220)
Q Consensus 72 k~vVCPVCa~~ 82 (220)
.-.+||.|.+.
T Consensus 34 ~v~~C~~Cg~~ 44 (236)
T PF04981_consen 34 EVTICPKCGRY 44 (236)
T ss_pred CceECCCCCCE
Confidence 45789999875
No 175
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.46 E-value=40 Score=36.08 Aligned_cols=44 Identities=27% Similarity=0.623 Sum_probs=37.2
Q ss_pred cCCCCCccchHH---HhhhhhhcccCCCcccccccccccc--cchhHhh
Q 027681 46 PCPFCYLEIEAH---MICSHLQEEHCFEMKNAVCPLCAAN--LGKDAAE 89 (220)
Q Consensus 46 ~CPfC~ed~D~~---~Lc~H~~eeH~~e~k~vVCPVCa~~--vg~D~i~ 89 (220)
+|--|.-.+|+. -+|-|.--.||++.+...||-|..- -++||++
T Consensus 842 kCs~C~~~LdlP~VhF~CgHsyHqhC~e~~~~~CP~C~~e~~~~m~l~~ 890 (933)
T KOG2114|consen 842 KCSACEGTLDLPFVHFLCGHSYHQHCLEDKEDKCPKCLPELRGVMDLKR 890 (933)
T ss_pred eecccCCccccceeeeecccHHHHHhhccCcccCCccchhhhhhHHHHH
Confidence 899998888865 5899999999999999999999983 3556655
No 176
>PF02934 GatB_N: GatB/GatE catalytic domain; InterPro: IPR006075 Glutamyl-tRNA(Gln) amidotransferase subunit B (6.3.5 from EC) [] is a microbial enzyme that furnishes a means for formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). The enzyme is composed of three subunits: A (an amidase), B and C. It also exists in eukaryotes as a protein targeted to the mitochondria. ; GO: 0016874 ligase activity; PDB: 3H0M_H 3H0R_K 3H0L_K 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B 2G5H_B 2DQN_B ....
Probab=20.44 E-value=47 Score=30.98 Aligned_cols=24 Identities=29% Similarity=0.513 Sum_probs=15.2
Q ss_pred hhhcccCCCcccccccccccccch
Q 027681 62 HLQEEHCFEMKNAVCPLCAANLGK 85 (220)
Q Consensus 62 H~~eeH~~e~k~vVCPVCa~~vg~ 85 (220)
.|..+...+++.-|||+|...+|.
T Consensus 21 ~c~~~~~~~pNt~v~~~~lg~PGt 44 (289)
T PF02934_consen 21 SCPNEFGAEPNTNVCPVCLGLPGT 44 (289)
T ss_dssp SSBSSTTSCTTSSB-TTTTT-TTC
T ss_pred CCCCCCCCCCccccCceeccCCCC
Confidence 344444447888999999999654
No 177
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=20.27 E-value=66 Score=20.74 Aligned_cols=31 Identities=19% Similarity=0.346 Sum_probs=16.9
Q ss_pred ecCCCCCccchHHHhhhhhhcccCCCccccccccccc
Q 027681 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (220)
Q Consensus 45 F~CPfC~ed~D~~~Lc~H~~eeH~~e~k~vVCPVCa~ 81 (220)
+.||-|...|++..-. =|-....+-||.|..
T Consensus 3 i~Cp~C~~~y~i~d~~------ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEK------IPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHHH------CCCCCcEEECCCCCC
Confidence 4688886655443211 133445667777754
No 178
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.21 E-value=46 Score=24.74 Aligned_cols=13 Identities=31% Similarity=0.938 Sum_probs=8.6
Q ss_pred Ccccccccccccc
Q 027681 70 EMKNAVCPLCAAN 82 (220)
Q Consensus 70 e~k~vVCPVCa~~ 82 (220)
+...++||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 4566777777664
No 179
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=20.03 E-value=48 Score=28.10 Aligned_cols=20 Identities=30% Similarity=0.665 Sum_probs=14.5
Q ss_pred hhcccCCCc--------------ccccccccccc
Q 027681 63 LQEEHCFEM--------------KNAVCPLCAAN 82 (220)
Q Consensus 63 ~~eeH~~e~--------------k~vVCPVCa~~ 82 (220)
|+..|.||. .-+.||+|-..
T Consensus 8 C~~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~ 41 (148)
T PF06676_consen 8 CENGHEFEGWFRSSAAFDRQQARGLVSCPVCGST 41 (148)
T ss_pred cCCCCccceecCCHHHHHHHHHcCCccCCCCCCC
Confidence 556677754 55779999886
Done!