Query 028361
Match_columns 210
No_of_seqs 149 out of 163
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 10:18:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028361.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028361hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14571 Di19_C: Stress-induce 99.9 2E-28 4.4E-33 190.7 6.8 93 115-209 2-105 (105)
2 PF05605 zf-Di19: Drought indu 99.8 7.9E-20 1.7E-24 125.9 4.1 54 43-96 1-54 (54)
3 KOG1280 Uncharacterized conser 97.9 8.3E-06 1.8E-10 75.4 3.3 42 42-83 77-119 (381)
4 KOG2923 Uncharacterized conser 95.0 0.008 1.7E-07 43.6 0.6 46 30-84 7-55 (67)
5 COG5216 Uncharacterized conser 94.3 0.016 3.5E-07 41.6 0.7 38 39-83 17-54 (67)
6 PF13894 zf-C2H2_4: C2H2-type 92.5 0.073 1.6E-06 29.1 1.3 23 45-67 1-24 (24)
7 PF09237 GAGA: GAGA factor; I 91.9 0.1 2.2E-06 36.5 1.6 28 70-97 21-50 (54)
8 PF13913 zf-C2HC_2: zinc-finge 91.6 0.12 2.7E-06 30.4 1.6 21 44-64 2-22 (25)
9 PF13909 zf-H2C2_5: C2H2-type 90.8 0.12 2.6E-06 29.3 1.0 24 45-68 1-24 (24)
10 PLN03086 PRLI-interacting fact 90.8 0.23 5E-06 49.2 3.5 46 43-93 452-498 (567)
11 PHA00732 hypothetical protein 89.9 0.28 6E-06 36.5 2.5 43 45-92 2-45 (79)
12 smart00531 TFIIE Transcription 89.0 0.24 5.2E-06 40.3 1.8 42 39-85 94-135 (147)
13 PRK09710 lar restriction allev 88.6 0.15 3.3E-06 36.9 0.3 33 44-85 6-39 (64)
14 KOG1842 FYVE finger-containing 88.3 0.2 4.3E-06 48.4 0.9 35 39-73 10-45 (505)
15 PF00096 zf-C2H2: Zinc finger, 88.2 0.22 4.7E-06 27.7 0.7 21 45-65 1-22 (23)
16 smart00834 CxxC_CXXC_SSSS Puta 88.0 0.16 3.4E-06 32.1 0.1 33 43-83 4-36 (41)
17 TIGR02098 MJ0042_CXXC MJ0042 f 87.5 0.24 5.2E-06 31.2 0.7 33 45-83 3-35 (38)
18 PF08274 PhnA_Zn_Ribbon: PhnA 87.4 0.19 4.1E-06 31.2 0.2 24 46-81 4-27 (30)
19 TIGR01206 lysW lysine biosynth 86.9 0.2 4.4E-06 35.0 0.1 30 44-82 2-31 (54)
20 PF12756 zf-C2H2_2: C2H2 type 86.6 0.35 7.6E-06 34.9 1.2 48 46-93 1-72 (100)
21 PF08271 TF_Zn_Ribbon: TFIIB z 86.3 0.21 4.6E-06 32.6 -0.1 34 45-88 1-34 (43)
22 PF14354 Lar_restr_allev: Rest 85.8 0.23 5.1E-06 34.1 -0.0 31 44-81 3-37 (61)
23 PF04780 DUF629: Protein of un 85.1 0.59 1.3E-05 45.4 2.3 51 41-91 54-105 (466)
24 PHA00733 hypothetical protein 85.0 1.2 2.5E-05 35.8 3.6 50 43-96 72-124 (128)
25 PF09986 DUF2225: Uncharacteri 84.3 0.29 6.3E-06 42.3 -0.2 50 43-92 4-67 (214)
26 PLN03208 E3 ubiquitin-protein 83.7 0.51 1.1E-05 40.9 1.1 47 41-87 15-82 (193)
27 KOG2462 C2H2-type Zn-finger pr 83.2 0.99 2.2E-05 41.1 2.8 38 41-82 158-196 (279)
28 COG5236 Uncharacterized conser 83.2 1.8 4E-05 41.0 4.6 62 41-108 217-318 (493)
29 KOG2462 C2H2-type Zn-finger pr 83.1 0.92 2E-05 41.3 2.5 52 41-92 127-182 (279)
30 smart00504 Ubox Modified RING 82.9 1.2 2.6E-05 30.1 2.5 33 50-89 19-52 (63)
31 TIGR02605 CxxC_CxxC_SSSS putat 82.7 0.42 9.2E-06 31.9 0.2 31 43-81 4-34 (52)
32 PF14255 Cys_rich_CPXG: Cystei 82.2 0.46 9.9E-06 33.0 0.2 34 45-83 1-34 (52)
33 PF14206 Cys_rich_CPCC: Cystei 81.3 0.5 1.1E-05 35.4 0.1 26 44-80 1-27 (78)
34 KOG0320 Predicted E3 ubiquitin 80.9 0.99 2.1E-05 38.9 1.8 46 42-87 129-181 (187)
35 smart00734 ZnF_Rad18 Rad18-lik 79.5 1.4 3E-05 26.2 1.6 20 45-64 2-21 (26)
36 PLN03086 PRLI-interacting fact 79.4 1.6 3.5E-05 43.4 2.9 39 43-84 477-515 (567)
37 PHA02768 hypothetical protein; 78.5 1.7 3.8E-05 30.5 2.1 34 44-81 5-39 (55)
38 PRK00398 rpoP DNA-directed RNA 78.5 1 2.2E-05 29.7 0.9 29 44-83 3-31 (46)
39 cd00350 rubredoxin_like Rubred 77.3 1.1 2.3E-05 27.8 0.7 25 45-82 2-26 (33)
40 PRK12496 hypothetical protein; 77.0 0.91 2E-05 37.9 0.4 28 44-84 127-154 (164)
41 PF12756 zf-C2H2_2: C2H2 type 77.0 1.4 3E-05 31.7 1.4 25 43-67 49-74 (100)
42 PF09723 Zn-ribbon_8: Zinc rib 76.3 0.57 1.2E-05 30.6 -0.8 31 43-81 4-34 (42)
43 PRK14892 putative transcriptio 74.4 1.1 2.3E-05 34.9 0.2 38 41-86 18-55 (99)
44 PF02176 zf-TRAF: TRAF-type zi 74.4 1.2 2.7E-05 30.0 0.5 46 43-90 8-60 (60)
45 PF04564 U-box: U-box domain; 71.5 6 0.00013 28.3 3.5 38 42-85 2-51 (73)
46 cd00729 rubredoxin_SM Rubredox 71.3 1.9 4.1E-05 27.1 0.8 26 44-82 2-27 (34)
47 COG4888 Uncharacterized Zn rib 71.1 1 2.2E-05 35.5 -0.7 37 41-82 19-55 (104)
48 PF05605 zf-Di19: Drought indu 70.6 3 6.5E-05 28.2 1.7 25 74-98 3-28 (54)
49 TIGR03655 anti_R_Lar restricti 70.1 1.9 4.2E-05 29.3 0.6 8 45-52 2-9 (53)
50 PF03145 Sina: Seven in absent 69.8 3 6.5E-05 35.1 1.9 54 43-99 13-75 (198)
51 PF05129 Elf1: Transcription e 69.7 1.9 4.1E-05 32.2 0.6 35 41-82 19-55 (81)
52 PF12773 DZR: Double zinc ribb 69.6 2.3 5E-05 28.0 0.9 28 46-85 14-41 (50)
53 PF07754 DUF1610: Domain of un 67.9 2.9 6.2E-05 24.8 1.0 12 41-52 13-24 (24)
54 PRK06266 transcription initiat 67.1 4.1 8.8E-05 34.5 2.1 36 40-85 113-148 (178)
55 TIGR00373 conserved hypothetic 67.1 4 8.7E-05 33.8 2.0 37 39-85 104-140 (158)
56 PF04423 Rad50_zn_hook: Rad50 66.4 3 6.5E-05 28.3 1.0 20 74-93 21-44 (54)
57 PF13465 zf-H2C2_2: Zinc-finge 66.3 1.8 3.9E-05 25.3 -0.1 10 45-54 15-24 (26)
58 PF07191 zinc-ribbons_6: zinc- 66.1 0.96 2.1E-05 33.3 -1.6 39 45-83 2-40 (70)
59 COG1655 Uncharacterized protei 66.0 2.2 4.8E-05 38.3 0.3 40 42-81 17-70 (267)
60 KOG2593 Transcription initiati 65.4 2.7 5.9E-05 40.5 0.8 43 34-83 118-163 (436)
61 KOG3623 Homeobox transcription 64.6 3.8 8.3E-05 42.2 1.7 41 42-82 208-249 (1007)
62 COG4049 Uncharacterized protei 64.0 3.1 6.8E-05 29.8 0.7 17 84-100 30-46 (65)
63 PTZ00255 60S ribosomal protein 63.7 1.9 4.1E-05 33.2 -0.4 15 38-52 30-44 (90)
64 PRK12495 hypothetical protein; 63.4 3.6 7.8E-05 36.5 1.1 31 42-85 40-70 (226)
65 COG1592 Rubrerythrin [Energy p 62.4 4.7 0.0001 34.1 1.6 25 44-82 134-158 (166)
66 COG2888 Predicted Zn-ribbon RN 61.8 6.1 0.00013 28.4 1.9 35 39-80 22-57 (61)
67 PF02892 zf-BED: BED zinc fing 60.8 4.4 9.5E-05 26.0 0.9 28 40-67 12-44 (45)
68 TIGR00686 phnA alkylphosphonat 59.6 3.8 8.2E-05 32.6 0.5 26 45-82 3-28 (109)
69 PF10571 UPF0547: Uncharacteri 59.5 5.5 0.00012 23.7 1.1 9 46-54 2-10 (26)
70 COG4311 SoxD Sarcosine oxidase 59.4 4.1 8.9E-05 31.7 0.7 9 44-52 3-11 (97)
71 PF13248 zf-ribbon_3: zinc-rib 59.3 5.8 0.00013 23.2 1.2 23 45-82 3-25 (26)
72 PF08996 zf-DNA_Pol: DNA Polym 58.8 2.6 5.5E-05 35.7 -0.6 42 42-85 16-57 (188)
73 PF13395 HNH_4: HNH endonuclea 58.2 5 0.00011 27.3 0.9 14 47-60 1-14 (54)
74 TIGR00100 hypA hydrogenase nic 57.4 4.2 9.1E-05 32.0 0.5 30 40-82 66-95 (115)
75 smart00614 ZnF_BED BED zinc fi 57.1 5.5 0.00012 26.5 0.9 26 43-68 17-48 (50)
76 TIGR00280 L37a ribosomal prote 57.1 2.8 6E-05 32.3 -0.6 15 38-52 29-43 (91)
77 smart00659 RPOLCX RNA polymera 57.0 5.1 0.00011 26.7 0.8 28 44-83 2-29 (44)
78 PF13240 zinc_ribbon_2: zinc-r 57.0 3.7 8E-05 23.7 0.1 8 47-54 2-9 (23)
79 PF08209 Sgf11: Sgf11 (transcr 56.9 6 0.00013 25.0 1.0 23 43-65 3-25 (33)
80 PF07282 OrfB_Zn_ribbon: Putat 56.9 11 0.00023 26.4 2.4 42 40-92 24-65 (69)
81 smart00355 ZnF_C2H2 zinc finge 56.7 9.1 0.0002 20.4 1.7 20 45-64 1-21 (26)
82 COG5175 MOT2 Transcriptional r 56.6 2.8 6E-05 39.8 -0.7 15 70-84 50-64 (480)
83 PF03470 zf-XS: XS zinc finger 56.6 7 0.00015 26.2 1.4 9 76-84 1-9 (43)
84 cd00730 rubredoxin Rubredoxin; 56.5 7 0.00015 26.8 1.4 13 40-52 30-42 (50)
85 PRK03976 rpl37ae 50S ribosomal 56.0 3.1 6.6E-05 32.1 -0.5 15 38-52 30-44 (90)
86 PF06957 COPI_C: Coatomer (COP 55.9 5.1 0.00011 38.5 0.9 34 43-89 379-413 (422)
87 PF01155 HypA: Hydrogenase exp 55.5 3.4 7.5E-05 32.3 -0.3 30 40-82 66-95 (113)
88 PRK03824 hypA hydrogenase nick 55.2 5.4 0.00012 32.2 0.8 43 40-82 66-116 (135)
89 smart00507 HNHc HNH nucleases. 55.2 2.8 6E-05 26.3 -0.7 21 45-65 11-31 (52)
90 PRK00420 hypothetical protein; 54.5 7.7 0.00017 30.9 1.5 27 45-83 24-50 (112)
91 PRK14890 putative Zn-ribbon RN 54.2 9 0.0002 27.4 1.7 34 40-80 21-55 (59)
92 PF00301 Rubredoxin: Rubredoxi 53.8 6.3 0.00014 26.7 0.8 14 39-52 29-42 (47)
93 KOG1002 Nucleotide excision re 52.7 6.9 0.00015 39.2 1.2 56 37-92 529-594 (791)
94 PF05876 Terminase_GpA: Phage 51.3 6.8 0.00015 38.5 0.9 43 42-86 198-242 (557)
95 PRK12380 hydrogenase nickel in 51.2 5.9 0.00013 31.1 0.4 31 39-82 65-95 (113)
96 PF11672 DUF3268: Protein of u 50.4 7.2 0.00016 30.6 0.8 39 45-85 3-43 (102)
97 PF01844 HNH: HNH endonuclease 50.2 2.2 4.8E-05 27.2 -1.8 37 47-83 1-44 (47)
98 PRK03922 hypothetical protein; 50.0 7.2 0.00016 31.2 0.7 15 44-58 49-63 (113)
99 COG0675 Transposase and inacti 50.0 12 0.00027 32.2 2.3 38 39-92 304-341 (364)
100 KOG2817 Predicted E3 ubiquitin 48.7 8.4 0.00018 36.8 1.1 13 44-56 374-386 (394)
101 PF04475 DUF555: Protein of un 48.5 7.8 0.00017 30.5 0.7 15 44-58 47-61 (102)
102 PF13912 zf-C2H2_6: C2H2-type 48.0 11 0.00024 21.4 1.1 21 45-65 2-23 (27)
103 PF14634 zf-RING_5: zinc-RING 46.6 15 0.00032 23.6 1.7 10 71-80 34-43 (44)
104 COG5109 Uncharacterized conser 46.4 8.5 0.00018 36.2 0.7 10 44-53 376-385 (396)
105 PHA00616 hypothetical protein 46.3 12 0.00027 25.1 1.3 21 45-65 2-23 (44)
106 PF13719 zinc_ribbon_5: zinc-r 45.9 11 0.00025 23.8 1.0 31 45-81 3-33 (37)
107 TIGR00570 cdk7 CDK-activating 45.5 11 0.00025 34.8 1.4 40 45-85 4-55 (309)
108 COG5189 SFP1 Putative transcri 45.3 11 0.00023 35.7 1.1 41 43-83 348-408 (423)
109 PF02146 SIR2: Sir2 family; I 44.9 11 0.00023 31.1 1.0 40 43-87 104-143 (178)
110 PRK10220 hypothetical protein; 44.1 12 0.00025 29.9 1.1 25 45-82 4-29 (111)
111 PRK11595 DNA utilization prote 43.8 13 0.00027 32.1 1.3 35 46-82 7-43 (227)
112 PF09538 FYDLN_acid: Protein o 43.8 11 0.00025 29.6 1.0 34 40-86 5-39 (108)
113 PRK11088 rrmA 23S rRNA methylt 43.7 7.6 0.00016 33.9 -0.0 32 44-75 2-34 (272)
114 COG2176 PolC DNA polymerase II 43.6 18 0.00039 39.4 2.6 41 40-85 910-951 (1444)
115 PF13717 zinc_ribbon_4: zinc-r 42.9 13 0.00028 23.5 1.0 31 45-81 3-33 (36)
116 COG4391 Uncharacterized protei 42.3 11 0.00023 27.3 0.5 13 42-54 46-58 (62)
117 PF01780 Ribosomal_L37ae: Ribo 41.8 11 0.00024 29.0 0.6 14 39-52 30-43 (90)
118 KOG2932 E3 ubiquitin ligase in 40.8 20 0.00042 33.8 2.1 28 73-100 123-176 (389)
119 PRK12860 transcriptional activ 40.7 20 0.00044 31.0 2.1 31 40-80 130-161 (189)
120 PHA02929 N1R/p28-like protein; 40.4 6.2 0.00013 35.1 -1.1 45 40-84 170-227 (238)
121 KOG3608 Zn finger proteins [Ge 40.3 27 0.00059 33.5 3.0 48 44-92 263-313 (467)
122 PF14570 zf-RING_4: RING/Ubox 39.9 12 0.00025 25.7 0.4 34 41-81 12-45 (48)
123 PF14279 HNH_5: HNH endonuclea 39.8 14 0.00031 26.9 0.9 41 47-92 1-49 (71)
124 COG1327 Predicted transcriptio 39.7 15 0.00033 30.9 1.1 33 46-84 2-39 (156)
125 PF12660 zf-TFIIIC: Putative z 39.6 6.4 0.00014 30.3 -1.0 39 45-83 15-65 (99)
126 PF15616 TerY-C: TerY-C metal 39.0 10 0.00022 31.0 -0.0 45 42-88 75-120 (131)
127 cd00162 RING RING-finger (Real 38.9 5.8 0.00013 23.9 -1.1 11 72-82 34-44 (45)
128 PF05207 zf-CSL: CSL zinc fing 38.5 12 0.00025 25.9 0.2 44 32-84 5-51 (55)
129 KOG2231 Predicted E3 ubiquitin 37.9 20 0.00042 36.6 1.8 29 41-69 179-208 (669)
130 PF13824 zf-Mss51: Zinc-finger 37.9 17 0.00036 25.6 0.9 12 41-52 11-22 (55)
131 TIGR00165 S18 ribosomal protei 37.7 21 0.00045 26.2 1.4 30 71-100 3-38 (70)
132 PF14311 DUF4379: Domain of un 36.9 20 0.00044 24.1 1.3 38 34-79 18-55 (55)
133 PRK04023 DNA polymerase II lar 36.8 17 0.00038 38.7 1.3 39 43-85 637-675 (1121)
134 PF10058 DUF2296: Predicted in 36.7 15 0.00033 25.4 0.6 10 43-52 43-52 (54)
135 COG1499 NMD3 NMD protein affec 36.4 20 0.00044 33.7 1.6 40 42-81 4-51 (355)
136 PF04267 SoxD: Sarcosine oxida 35.7 11 0.00024 28.6 -0.3 8 45-52 2-9 (84)
137 KOG2879 Predicted E3 ubiquitin 35.6 11 0.00023 34.8 -0.4 41 43-83 238-286 (298)
138 COG5415 Predicted integral mem 35.4 27 0.00058 31.2 2.0 38 40-84 188-225 (251)
139 PF09862 DUF2089: Protein of u 34.7 8.8 0.00019 30.6 -1.0 13 47-59 1-13 (113)
140 PF10609 ParA: ParA/MinD ATPas 34.5 13 0.00028 28.0 -0.1 18 39-56 60-77 (81)
141 TIGR01374 soxD sarcosine oxida 33.6 19 0.00041 27.4 0.7 8 45-52 2-9 (84)
142 KOG3214 Uncharacterized Zn rib 33.0 18 0.00038 28.7 0.5 33 41-82 20-56 (109)
143 KOG2893 Zn finger protein [Gen 32.7 20 0.00043 32.7 0.8 30 47-82 13-43 (341)
144 cd03021 DsbA_GSTK DsbA family, 32.6 9.3 0.0002 32.1 -1.2 14 40-53 4-17 (209)
145 PF14616 DUF4451: Domain of un 31.9 23 0.00051 28.2 1.1 26 73-98 25-55 (124)
146 PF11290 DUF3090: Protein of u 31.9 21 0.00045 30.5 0.8 14 45-58 155-168 (171)
147 PHA02565 49 recombination endo 31.8 19 0.00041 30.4 0.5 41 44-84 20-66 (157)
148 cd03024 DsbA_FrnE DsbA family, 31.5 13 0.00028 30.2 -0.5 23 41-63 3-26 (201)
149 PF14471 DUF4428: Domain of un 31.5 12 0.00025 25.6 -0.6 30 46-83 1-30 (51)
150 PRK05654 acetyl-CoA carboxylas 31.3 31 0.00067 31.5 1.8 29 44-82 27-55 (292)
151 PF14353 CpXC: CpXC protein 31.2 21 0.00045 27.9 0.7 16 42-57 36-51 (128)
152 PF13453 zf-TFIIB: Transcripti 31.1 15 0.00033 23.5 -0.1 27 46-81 1-27 (41)
153 PF14447 Prok-RING_4: Prokaryo 30.6 16 0.00035 25.7 -0.0 43 42-84 5-50 (55)
154 PRK03681 hypA hydrogenase nick 30.5 17 0.00036 28.5 -0.0 31 40-82 66-96 (114)
155 PF09334 tRNA-synt_1g: tRNA sy 30.4 14 0.0003 34.7 -0.6 40 44-83 136-176 (391)
156 PF00097 zf-C3HC4: Zinc finger 30.3 8.7 0.00019 23.9 -1.4 9 71-79 33-41 (41)
157 PF10276 zf-CHCC: Zinc-finger 30.2 20 0.00044 23.5 0.3 10 44-53 29-38 (40)
158 KOG2177 Predicted E3 ubiquitin 30.1 22 0.00048 29.1 0.6 40 41-80 10-54 (386)
159 KOG2114 Vacuolar assembly/sort 30.0 22 0.00048 37.2 0.8 44 46-89 842-890 (933)
160 PRK00464 nrdR transcriptional 29.9 22 0.00048 29.6 0.6 33 45-83 1-38 (154)
161 TIGR00515 accD acetyl-CoA carb 29.7 35 0.00076 31.1 1.9 29 44-82 26-54 (285)
162 COG2761 FrnE Predicted dithiol 29.6 38 0.00083 30.0 2.1 52 40-97 9-69 (225)
163 CHL00174 accD acetyl-CoA carbo 29.5 50 0.0011 30.4 2.9 29 44-82 38-66 (296)
164 PRK00564 hypA hydrogenase nick 29.1 23 0.0005 27.9 0.6 31 40-82 67-97 (117)
165 COG1198 PriA Primosomal protei 29.0 24 0.00051 36.3 0.8 41 40-82 440-484 (730)
166 TIGR00599 rad18 DNA repair pro 28.9 15 0.00033 35.1 -0.6 47 39-85 21-72 (397)
167 cd03022 DsbA_HCCA_Iso DsbA fam 28.8 12 0.00026 30.0 -1.1 15 41-55 3-17 (192)
168 PRK00423 tfb transcription ini 28.7 29 0.00063 31.5 1.2 41 41-91 8-48 (310)
169 COG1996 RPC10 DNA-directed RNA 28.6 28 0.0006 24.0 0.8 12 41-52 21-32 (49)
170 PF12230 PRP21_like_P: Pre-mRN 27.9 20 0.00043 30.9 0.0 19 45-63 169-187 (229)
171 PF09706 Cas_CXXC_CXXC: CRISPR 27.8 25 0.00053 25.4 0.5 11 42-52 3-13 (69)
172 PF03604 DNA_RNApol_7kD: DNA d 27.6 36 0.00078 21.2 1.1 14 39-52 12-25 (32)
173 PRK12722 transcriptional activ 27.3 47 0.001 28.7 2.2 32 40-81 130-162 (187)
174 TIGR00618 sbcc exonuclease Sbc 27.1 20 0.00044 37.6 -0.1 33 41-85 498-536 (1042)
175 PF11793 FANCL_C: FANCL C-term 26.9 35 0.00076 24.4 1.1 46 40-85 16-67 (70)
176 COG1997 RPL43A Ribosomal prote 26.8 16 0.00035 28.1 -0.6 17 37-53 28-44 (89)
177 COG1885 Uncharacterized protei 26.8 29 0.00063 27.7 0.8 16 44-59 49-64 (115)
178 TIGR03278 methan_mark_10 putat 26.6 23 0.0005 33.7 0.2 35 43-83 9-46 (404)
179 cd02972 DsbA_family DsbA famil 26.6 18 0.00039 24.8 -0.4 10 43-52 5-14 (98)
180 PF03966 Trm112p: Trm112p-like 26.2 40 0.00088 23.7 1.4 19 43-61 6-24 (68)
181 cd03019 DsbA_DsbA DsbA family, 26.0 24 0.00053 27.8 0.2 18 43-60 23-41 (178)
182 KOG0402 60S ribosomal protein 26.0 21 0.00045 27.5 -0.2 13 40-52 32-44 (92)
183 PRK14873 primosome assembly pr 25.8 29 0.00062 35.2 0.7 39 40-82 388-431 (665)
184 COG1675 TFA1 Transcription ini 25.5 49 0.0011 28.3 2.0 35 41-85 110-144 (176)
185 PF14968 CCDC84: Coiled coil p 25.5 35 0.00076 32.0 1.2 20 38-57 52-71 (336)
186 PF12760 Zn_Tnp_IS1595: Transp 25.1 39 0.00084 22.1 1.0 11 42-52 16-26 (46)
187 PF06221 zf-C2HC5: Putative zi 25.0 34 0.00074 24.1 0.8 10 44-53 35-44 (57)
188 KOG4080 Mitochondrial ribosoma 24.9 32 0.0007 29.5 0.7 26 44-85 93-118 (176)
189 KOG4696 Uncharacterized conser 24.9 40 0.00087 31.7 1.4 23 44-67 2-24 (393)
190 KOG3623 Homeobox transcription 24.7 35 0.00075 35.6 1.0 68 44-113 894-968 (1007)
191 smart00451 ZnF_U1 U1-like zinc 24.6 50 0.0011 19.5 1.4 19 45-63 4-23 (35)
192 PF12171 zf-C2H2_jaz: Zinc-fin 24.4 47 0.001 19.0 1.2 19 45-63 2-21 (27)
193 KOG3002 Zn finger protein [Gen 24.2 23 0.0005 32.5 -0.2 44 41-84 45-91 (299)
194 TIGR00630 uvra excinuclease AB 23.6 44 0.00095 35.2 1.6 35 42-81 248-282 (924)
195 PF04981 NMD3: NMD3 family ; 23.3 45 0.00098 29.0 1.4 11 72-82 34-44 (236)
196 PF08273 Prim_Zn_Ribbon: Zinc- 23.3 34 0.00075 22.4 0.5 8 45-52 4-11 (40)
197 PF02891 zf-MIZ: MIZ/SP-RING z 23.1 11 0.00023 25.5 -2.0 8 74-81 42-49 (50)
198 PRK09678 DNA-binding transcrip 23.1 38 0.00083 24.9 0.7 8 45-52 2-9 (72)
199 PF13462 Thioredoxin_4: Thiore 23.1 16 0.00034 28.3 -1.4 21 43-63 20-41 (162)
200 PRK14714 DNA polymerase II lar 23.0 38 0.00081 37.1 0.9 21 186-206 839-859 (1337)
201 TIGR01405 polC_Gram_pos DNA po 22.9 54 0.0012 35.7 2.1 47 31-85 673-720 (1213)
202 PF14369 zf-RING_3: zinc-finge 22.5 41 0.00088 21.2 0.7 9 46-54 23-31 (35)
203 PRK14714 DNA polymerase II lar 22.3 38 0.00083 37.0 0.9 21 44-65 667-687 (1337)
204 PF01323 DSBA: DSBA-like thior 22.2 14 0.00031 29.5 -1.8 19 42-60 5-24 (193)
205 TIGR00595 priA primosomal prot 22.0 36 0.00078 33.1 0.6 37 43-82 221-262 (505)
206 TIGR02300 FYDLN_acid conserved 21.9 43 0.00093 27.4 0.9 34 40-86 5-39 (129)
207 TIGR00244 transcriptional regu 21.8 39 0.00084 28.2 0.6 32 46-84 2-39 (147)
208 PRK05477 gatB aspartyl/glutamy 21.8 39 0.00084 33.0 0.7 21 65-85 29-49 (474)
209 PF14828 Amnionless: Amnionles 21.7 44 0.00095 32.2 1.1 41 45-86 192-239 (437)
210 KOG4445 Uncharacterized conser 21.5 22 0.00047 33.4 -1.0 19 67-85 169-187 (368)
211 PF03811 Zn_Tnp_IS1: InsA N-te 21.1 43 0.00093 21.4 0.6 9 44-52 5-13 (36)
212 PF04780 DUF629: Protein of un 20.5 51 0.0011 32.3 1.2 27 74-100 58-86 (466)
213 PF10825 DUF2752: Protein of u 20.5 45 0.00097 22.7 0.6 9 44-52 9-17 (52)
214 PRK00391 rpsR 30S ribosomal pr 20.4 65 0.0014 24.1 1.5 29 71-99 12-46 (79)
215 PRK00448 polC DNA polymerase I 20.3 65 0.0014 35.7 2.1 47 31-85 898-945 (1437)
216 PF03833 PolC_DP2: DNA polymer 20.2 34 0.00074 35.9 0.0 9 44-52 655-663 (900)
No 1
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=99.95 E-value=2e-28 Score=190.66 Aligned_cols=93 Identities=32% Similarity=0.481 Sum_probs=68.3
Q ss_pred cchhhhh-----hhhhcCCCCCCCCCCCCCCCCCcccccccCCCCCCCCCCCCcccCcccccccccc--ccCCCC----C
Q 028361 115 SAMLGKE-----LSSFLGSPTIVRGNAPESLPDPLLSPFLCSGTLSDTKGIQKDDCTNKFSLASDLK--SAGGTL----L 183 (210)
Q Consensus 115 ~sll~Ke-----lqsllgg~~~s~~~ssn~~pDPLLSsFi~n~~~~~~~~~e~~~s~~~~~~~~~~~--~~~~~~----~ 183 (210)
+++|+|| ||+||||+++++++++|++|||||||||||+|.++.. +..+....+..+...+ ..++.| .
T Consensus 2 lsll~kelre~~LQsllGgs~~~~~~ssn~apDPLLSSFI~n~~~~~~~--~~~~~~~~~~~~~s~~~~~~~~~~~~s~~ 79 (105)
T PF14571_consen 2 LSLLRKELREGYLQSLLGGSRSSSSSSSNSAPDPLLSSFICNFPAPEAE--EPSKSSSSSEEKKSSKKSSSEQNVKSSAD 79 (105)
T ss_pred cchhhhhhhhhhhhhhcCCCcCCCCCCCCCCCcHHHHHHhcCCCCcccc--ccCCccccccccccccccchhcccccccC
Confidence 5689999 5999999856677899999999999999999998733 2111111111111111 113334 4
Q ss_pred CCCChhHHHHHHhHhHHHHHHHhhhc
Q 028361 184 DDGHEENIEEKMQRATFVQQLIMSTV 209 (210)
Q Consensus 184 ~~ls~~d~eEr~~R~eFVQgLllSTi 209 (210)
++++++|+|||+||++||||||||||
T Consensus 80 ~~lS~ee~eEk~~RseFVQ~LllSTI 105 (105)
T PF14571_consen 80 SSLSDEEQEEKAQRSEFVQGLLLSTI 105 (105)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhC
Confidence 78999999999999999999999998
No 2
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=99.79 E-value=7.9e-20 Score=125.90 Aligned_cols=54 Identities=31% Similarity=0.711 Sum_probs=52.2
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhhhHHhhHhhhhc
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHFMVQHA 96 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d~i~Hi~~qh~ 96 (210)
.+|+||||+++||+.+|+.|++++|+.+.+++|||||+.+++.||++||+.+||
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 369999999999999999999999999999999999999999999999999996
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=97.89 E-value=8.3e-06 Score=75.43 Aligned_cols=42 Identities=31% Similarity=0.729 Sum_probs=39.1
Q ss_pred cccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 42 KACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 42 ~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
...|.||||+. +|....+.+|+..+|+.-...+|||||+...
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~ 119 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANP 119 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCc
Confidence 34899999999 9999999999999999999999999999974
No 4
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.04 E-value=0.008 Score=43.58 Aligned_cols=46 Identities=22% Similarity=0.486 Sum_probs=29.9
Q ss_pred CccCccccC-ccccccccCCCCCcchhHH--HhHhhhhhccCCCcccccCcccccchh
Q 028361 30 SIVDETEID-DDVKACFPCPFCYLEIEAH--MICSHLQEEHCFEMKNAVCPLCAANLG 84 (210)
Q Consensus 30 ~~~~~~~~d-~d~~~~f~CP~C~e~~d~~--~L~~H~~~eH~~e~~~~vCPvC~~~v~ 84 (210)
..|+|++=| +....+|||| ||..|.+. .|. .--..+.||-|+-.+.
T Consensus 7 Veiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I~ 55 (67)
T KOG2923|consen 7 VEIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLIIR 55 (67)
T ss_pred EEeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEEE
Confidence 345677634 4456799999 99865543 232 2245688999998754
No 5
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.32 E-value=0.016 Score=41.61 Aligned_cols=38 Identities=26% Similarity=0.550 Sum_probs=25.0
Q ss_pred ccccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 39 ~d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
++...+|||| ||.-|++. +++ -..--+.++||-|.-.|
T Consensus 17 e~~~ftyPCP-CGDRFeIs-----LeD-l~~GE~VArCPSCSLiv 54 (67)
T COG5216 17 EEKTFTYPCP-CGDRFEIS-----LED-LRNGEVVARCPSCSLIV 54 (67)
T ss_pred CCceEEecCC-CCCEeEEE-----HHH-hhCCceEEEcCCceEEE
Confidence 3456799999 99866553 111 12234568999999875
No 6
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=92.48 E-value=0.073 Score=29.11 Aligned_cols=23 Identities=26% Similarity=0.595 Sum_probs=14.5
Q ss_pred ccCCCCCc-chhHHHhHhhhhhcc
Q 028361 45 FPCPFCYL-EIEAHMICSHLQEEH 67 (210)
Q Consensus 45 f~CP~C~e-~~d~~~L~~H~~~eH 67 (210)
|.||+|+. --+...|..|+...|
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 67888887 445667777776654
No 7
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=91.86 E-value=0.1 Score=36.52 Aligned_cols=28 Identities=25% Similarity=0.672 Sum_probs=18.4
Q ss_pred CcccccCcccccch--hhhHHhhHhhhhcc
Q 028361 70 EMKNAVCPLCAANL--GKDAAEHFMVQHAS 97 (210)
Q Consensus 70 e~~~~vCPvC~~~v--~~d~i~Hi~~qh~~ 97 (210)
....+.||+|...+ .+|+-+|+.+.|+.
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 34456999999975 56999999988864
No 8
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.63 E-value=0.12 Score=30.37 Aligned_cols=21 Identities=24% Similarity=0.608 Sum_probs=18.7
Q ss_pred cccCCCCCcchhHHHhHhhhh
Q 028361 44 CFPCPFCYLEIEAHMICSHLQ 64 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~ 64 (210)
..+||+|+.-|....|-.|+.
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 578999999999999999964
No 9
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=90.81 E-value=0.12 Score=29.31 Aligned_cols=24 Identities=25% Similarity=0.627 Sum_probs=16.6
Q ss_pred ccCCCCCcchhHHHhHhhhhhccC
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHC 68 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~ 68 (210)
|.||+|...-....|..|+...|+
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 689999873347788888887775
No 10
>PLN03086 PRLI-interacting factor K; Provisional
Probab=90.79 E-value=0.23 Score=49.18 Aligned_cols=46 Identities=20% Similarity=0.399 Sum_probs=35.5
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchh-hhHHhhHhh
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG-KDAAEHFMV 93 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~-~d~i~Hi~~ 93 (210)
.-+.||+|++.|....|-.|....| +...|| |...+. .++..|++.
T Consensus 452 ~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~t 498 (567)
T PLN03086 452 NHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQAS 498 (567)
T ss_pred cCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhc
Confidence 3468999999888899999988855 678999 975543 477778763
No 11
>PHA00732 hypothetical protein
Probab=89.87 E-value=0.28 Score=36.50 Aligned_cols=43 Identities=26% Similarity=0.711 Sum_probs=33.1
Q ss_pred ccCCCCCcch-hHHHhHhhhhhccCCCcccccCcccccchhhhHHhhHh
Q 028361 45 FPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHFM 92 (210)
Q Consensus 45 f~CP~C~e~~-d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d~i~Hi~ 92 (210)
|+|+.|++.| ....|..|+...|.- ..|++|...-. .+..|++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~-~l~~H~~ 45 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR-RLNQHFY 45 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC-Chhhhhc
Confidence 7899999955 678899998754542 26999998766 6777775
No 12
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.05 E-value=0.24 Score=40.32 Aligned_cols=42 Identities=21% Similarity=0.426 Sum_probs=28.1
Q ss_pred ccccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 39 ~d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
+.....|.||.|+.-|+...-....+ + ...-+||.|...+-.
T Consensus 94 e~~~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 94 ETNNAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEELEE 135 (147)
T ss_pred ccCCcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEEEE
Confidence 34577999999998666544333221 2 344899999988643
No 13
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=88.57 E-value=0.15 Score=36.87 Aligned_cols=33 Identities=27% Similarity=0.564 Sum_probs=22.6
Q ss_pred cccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 44 CFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 44 ~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
.-|||||+. .+.+. |..-..-++|.-|.+....
T Consensus 6 lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 6 VKPCPFCGCPSVTVK---------AISGYYRAKCNGCESRTGY 39 (64)
T ss_pred ccCCCCCCCceeEEE---------ecCceEEEEcCCCCcCccc
Confidence 469999998 55443 2333445999999997443
No 14
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=88.29 E-value=0.2 Score=48.42 Aligned_cols=35 Identities=29% Similarity=0.600 Sum_probs=30.5
Q ss_pred ccccccccCCCCCcchh-HHHhHhhhhhccCCCccc
Q 028361 39 DDVKACFPCPFCYLEIE-AHMICSHLQEEHCFEMKN 73 (210)
Q Consensus 39 ~d~~~~f~CP~C~e~~d-~~~L~~H~~~eH~~e~~~ 73 (210)
++.+.-|-||+|.++|+ ...|-+|++.+|+.|-..
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 56788999999999875 678999999999998764
No 15
>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=88.23 E-value=0.22 Score=27.68 Aligned_cols=21 Identities=19% Similarity=0.621 Sum_probs=13.0
Q ss_pred ccCCCCCcch-hHHHhHhhhhh
Q 028361 45 FPCPFCYLEI-EAHMICSHLQE 65 (210)
Q Consensus 45 f~CP~C~e~~-d~~~L~~H~~~ 65 (210)
|.||.|+.-| +...|..|+..
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 5677777733 45566666654
No 16
>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=87.99 E-value=0.16 Score=32.09 Aligned_cols=33 Identities=21% Similarity=0.386 Sum_probs=23.3
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
.+|.||-|+..|++..-. .+....+||.|...+
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 579999999988754321 114567899998854
No 17
>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=87.50 E-value=0.24 Score=31.18 Aligned_cols=33 Identities=15% Similarity=0.229 Sum_probs=21.2
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
+.||.|+..|.+..-. .+.....+.||.|...+
T Consensus 3 ~~CP~C~~~~~v~~~~------~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQ------LGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHH------cCCCCCEEECCCCCCEE
Confidence 6899999866665422 22233467899997653
No 18
>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=87.44 E-value=0.19 Score=31.22 Aligned_cols=24 Identities=33% Similarity=0.690 Sum_probs=12.9
Q ss_pred cCCCCCcchhHHHhHhhhhhccCCCcccccCccccc
Q 028361 46 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 46 ~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
+||.|+.++.. .|....|||-|..
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 79999886655 5567789999974
No 19
>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=86.95 E-value=0.2 Score=34.98 Aligned_cols=30 Identities=33% Similarity=0.520 Sum_probs=21.7
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
.|.||-|++.|++..... .-.+.||.|.+.
T Consensus 2 ~~~CP~CG~~iev~~~~~---------GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL---------GELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCcc---------CCEEeCCCCCCE
Confidence 589999999887654321 225789999876
No 20
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=86.64 E-value=0.35 Score=34.91 Aligned_cols=48 Identities=23% Similarity=0.582 Sum_probs=14.4
Q ss_pred cCCCCCcc-hhHHHhHhhhhhccCCCcc---------------------cccCcccccch--hhhHHhhHhh
Q 028361 46 PCPFCYLE-IEAHMICSHLQEEHCFEMK---------------------NAVCPLCAANL--GKDAAEHFMV 93 (210)
Q Consensus 46 ~CP~C~e~-~d~~~L~~H~~~eH~~e~~---------------------~~vCPvC~~~v--~~d~i~Hi~~ 93 (210)
.|+||+.. -++..|..|+...|.+... .-.|++|.... ...+..||+.
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 49999885 4578899999999987432 12399999985 4588899984
No 21
>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=86.29 E-value=0.21 Score=32.58 Aligned_cols=34 Identities=26% Similarity=0.509 Sum_probs=21.8
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhhhHH
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAA 88 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d~i 88 (210)
|.||.|+... + +.| ......||+.|..-+..+.+
T Consensus 1 m~Cp~Cg~~~-~------~~D---~~~g~~vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 1 MKCPNCGSKE-I------VFD---PERGELVCPNCGLVLEENII 34 (43)
T ss_dssp ESBTTTSSSE-E------EEE---TTTTEEEETTT-BBEE-TTB
T ss_pred CCCcCCcCCc-e------EEc---CCCCeEECCCCCCEeecccc
Confidence 6899998743 2 111 44566799999887776655
No 22
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=85.82 E-value=0.23 Score=34.13 Aligned_cols=31 Identities=29% Similarity=0.682 Sum_probs=19.0
Q ss_pred cccCCCCCc-chhHHHhHhhhhhccCCCc---ccccCccccc
Q 028361 44 CFPCPFCYL-EIEAHMICSHLQEEHCFEM---KNAVCPLCAA 81 (210)
Q Consensus 44 ~f~CP~C~e-~~d~~~L~~H~~~eH~~e~---~~~vCPvC~~ 81 (210)
..||||||. .+-+.. ....+. ..+.|..|..
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 468999986 443332 122221 5577999977
No 23
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=85.09 E-value=0.59 Score=45.36 Aligned_cols=51 Identities=24% Similarity=0.312 Sum_probs=36.9
Q ss_pred ccccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccchhhhHHhhH
Q 028361 41 VKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHF 91 (210)
Q Consensus 41 ~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d~i~Hi 91 (210)
-+.--.||+|.+ -.|..++..|+..+|+..-.+-.=++...+++.+-++.|
T Consensus 54 sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~~w~e~I 105 (466)
T PF04780_consen 54 SWRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDDDWAEMI 105 (466)
T ss_pred ceeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCHHHHHHH
Confidence 345678999998 899999999999999998766333344445554444444
No 24
>PHA00733 hypothetical protein
Probab=85.01 E-value=1.2 Score=35.82 Aligned_cols=50 Identities=20% Similarity=0.622 Sum_probs=36.0
Q ss_pred ccccCCCCCcchh-HHHhHhhhhhccCCCcccccCcccccch--hhhHHhhHhhhhc
Q 028361 43 ACFPCPFCYLEIE-AHMICSHLQEEHCFEMKNAVCPLCAANL--GKDAAEHFMVQHA 96 (210)
Q Consensus 43 ~~f~CP~C~e~~d-~~~L~~H~~~eH~~e~~~~vCPvC~~~v--~~d~i~Hi~~qh~ 96 (210)
..|.|+.|+..|. ...|..|..- | ..+..|++|.... ...+..|+.-.|+
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~-h---~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRY-T---EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhc-C---CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 3589999999655 4567788763 2 1346999998874 4488899886665
No 25
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=84.28 E-value=0.29 Score=42.35 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=30.5
Q ss_pred ccccCCCCCcchhHHHhHh--------------hhhhccCCCcccccCcccccchhhhHHhhHh
Q 028361 43 ACFPCPFCYLEIEAHMICS--------------HLQEEHCFEMKNAVCPLCAANLGKDAAEHFM 92 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~--------------H~~~eH~~e~~~~vCPvC~~~v~~d~i~Hi~ 92 (210)
-++.||+|+..|....+.. |-.+.-|+==...|||-|.---......+++
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~ 67 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLS 67 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccccccccCC
Confidence 3689999999998764433 3233333333457899998764443333444
No 26
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=83.74 E-value=0.51 Score=40.85 Aligned_cols=47 Identities=19% Similarity=0.594 Sum_probs=29.6
Q ss_pred ccccccCCCCCcchh--HHHhHhhh-----hhccC--------------CCcccccCcccccchhhhH
Q 028361 41 VKACFPCPFCYLEIE--AHMICSHL-----QEEHC--------------FEMKNAVCPLCAANLGKDA 87 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d--~~~L~~H~-----~~eH~--------------~e~~~~vCPvC~~~v~~d~ 87 (210)
....|.||.|.+.+. +...|-|+ -...- ...+...||+|...++.+-
T Consensus 15 ~~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 15 SGGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CCCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 446799999987443 44567772 22211 0223468999999987643
No 27
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=83.21 E-value=0.99 Score=41.11 Aligned_cols=38 Identities=21% Similarity=0.590 Sum_probs=28.6
Q ss_pred ccccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 41 VKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 41 ~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
.+..|.||+|++ ...+..|.-||-. |.. .-+|+||.+.
T Consensus 158 s~ka~~C~~C~K~YvSmpALkMHirT-H~l---~c~C~iCGKa 196 (279)
T KOG2462|consen 158 SKKAFSCKYCGKVYVSMPALKMHIRT-HTL---PCECGICGKA 196 (279)
T ss_pred ccccccCCCCCceeeehHHHhhHhhc-cCC---Cccccccccc
Confidence 377899999998 8888899988866 552 4467777665
No 28
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.17 E-value=1.8 Score=41.04 Aligned_cols=62 Identities=21% Similarity=0.351 Sum_probs=45.6
Q ss_pred ccccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccc-------------------------------hhh---
Q 028361 41 VKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN-------------------------------LGK--- 85 (210)
Q Consensus 41 ~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~-------------------------------v~~--- 85 (210)
..---.|-||.. =||-..|..||.+.|- .|-||+.. +|+
T Consensus 217 FKGHP~C~FC~~~FYdDDEL~~HcR~~HE------~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~v 290 (493)
T COG5236 217 FKGHPLCIFCKIYFYDDDELRRHCRLRHE------ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYV 290 (493)
T ss_pred cCCCchhhhccceecChHHHHHHHHhhhh------hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEE
Confidence 455667999988 7899999999998774 46777653 222
Q ss_pred -----hHHhhHhhhhcchhhhhhccccC
Q 028361 86 -----DAAEHFMVQHASSLKRRRKCLKS 108 (210)
Q Consensus 86 -----d~i~Hi~~qh~~~~Krr~r~rk~ 108 (210)
.+..||+..|+..+|..-+++.+
T Consensus 291 f~~~~el~~h~~~~h~~~~~~~~~~~~~ 318 (493)
T COG5236 291 FPYHTELLEHLTRFHKVNARLSEIPRPG 318 (493)
T ss_pred eccHHHHHHHHHHHhhcccccCcCCCCc
Confidence 67888888888888766555533
No 29
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=83.06 E-value=0.92 Score=41.32 Aligned_cols=52 Identities=17% Similarity=0.334 Sum_probs=28.7
Q ss_pred ccccccCCCCCc-chhHHHhHhhhhhccCCCc-ccccCcccccc-hhh-hHHhhHh
Q 028361 41 VKACFPCPFCYL-EIEAHMICSHLQEEHCFEM-KNAVCPLCAAN-LGK-DAAEHFM 92 (210)
Q Consensus 41 ~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~-~~~vCPvC~~~-v~~-d~i~Hi~ 92 (210)
....|.||-|+. .=...+|-.|-+..=+.+. +.-.|++|.+- |.+ -+-.||+
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHir 182 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIR 182 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhh
Confidence 345677777776 4455567777666334443 33557777664 333 3444554
No 30
>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=82.90 E-value=1.2 Score=30.10 Aligned_cols=33 Identities=18% Similarity=0.123 Sum_probs=22.7
Q ss_pred CCcchhHHHhHhhhhhccCCCcccccCcccccchhh-hHHh
Q 028361 50 CYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK-DAAE 89 (210)
Q Consensus 50 C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~-d~i~ 89 (210)
||.-|+...+..++.. +..||+|...++. |++.
T Consensus 19 ~G~v~~~~~i~~~~~~-------~~~cP~~~~~~~~~~l~~ 52 (63)
T smart00504 19 SGQTYERRAIEKWLLS-------HGTDPVTGQPLTHEDLIP 52 (63)
T ss_pred CCCEEeHHHHHHHHHH-------CCCCCCCcCCCChhhcee
Confidence 3455777777777755 4689999988754 4443
No 31
>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=82.67 E-value=0.42 Score=31.91 Aligned_cols=31 Identities=23% Similarity=0.519 Sum_probs=22.3
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCccccc
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
.+|.|+-|+..|++. ....+ .....||.|..
T Consensus 4 Yey~C~~Cg~~fe~~---~~~~~-----~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVL---QKMSD-----DPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEE---EecCC-----CCCCCCCCCCC
Confidence 579999999988853 12222 35578999997
No 32
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=82.24 E-value=0.46 Score=32.96 Aligned_cols=34 Identities=21% Similarity=0.424 Sum_probs=20.6
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
+.|||||+.+++. .+.-.. ...+.-=|+||-..+
T Consensus 1 i~CPyCge~~~~~--iD~s~~---~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 1 IQCPYCGEPIEIL--IDPSAG---DQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCCeeEEE--EecCCC---CeeEEeehhhcCCcc
Confidence 4799999977763 232222 222334599998764
No 33
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=81.30 E-value=0.5 Score=35.38 Aligned_cols=26 Identities=31% Similarity=0.826 Sum_probs=16.3
Q ss_pred cccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccc
Q 028361 44 CFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCA 80 (210)
Q Consensus 44 ~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~ 80 (210)
.|+||-|+. -|+..+- ..--|||||-
T Consensus 1 K~~CPCCg~~Tl~~~~~-----------~~ydIC~VC~ 27 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERGE-----------GTYDICPVCF 27 (78)
T ss_pred CccCCCCCcEEeccCCC-----------cCceECCCCC
Confidence 379999976 5543321 1123999996
No 34
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.92 E-value=0.99 Score=38.89 Aligned_cols=46 Identities=20% Similarity=0.649 Sum_probs=27.9
Q ss_pred cccccCCCCCcchhHH----HhHhhhhhccCC---CcccccCcccccchhhhH
Q 028361 42 KACFPCPFCYLEIEAH----MICSHLQEEHCF---EMKNAVCPLCAANLGKDA 87 (210)
Q Consensus 42 ~~~f~CP~C~e~~d~~----~L~~H~~~eH~~---e~~~~vCPvC~~~v~~d~ 87 (210)
.+.|.||.|-..+... .=|=|+-=.-|. -.+..+||+|.++|+.-.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~ 181 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQ 181 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchhh
Confidence 4679999997655433 334443222222 124578999999987643
No 35
>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=79.52 E-value=1.4 Score=26.17 Aligned_cols=20 Identities=40% Similarity=0.982 Sum_probs=11.6
Q ss_pred ccCCCCCcchhHHHhHhhhh
Q 028361 45 FPCPFCYLEIEAHMICSHLQ 64 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~ 64 (210)
++||-|++.+....+-.|++
T Consensus 2 v~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVPENLINSHLD 21 (26)
T ss_pred CcCCCCcCcccHHHHHHHHH
Confidence 35666666555555556654
No 36
>PLN03086 PRLI-interacting factor K; Provisional
Probab=79.37 E-value=1.6 Score=43.36 Aligned_cols=39 Identities=21% Similarity=0.548 Sum_probs=27.7
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchh
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 84 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~ 84 (210)
..+.|| |+..+.-..|-.|+.. |+-. +...|+.|...+.
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~t-hCp~-Kpi~C~fC~~~v~ 515 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQAS-TCPL-RLITCRFCGDMVQ 515 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhhc-cCCC-CceeCCCCCCccc
Confidence 457788 8777777888888754 5543 6678888877763
No 37
>PHA02768 hypothetical protein; Provisional
Probab=78.50 E-value=1.7 Score=30.49 Aligned_cols=34 Identities=24% Similarity=0.501 Sum_probs=22.8
Q ss_pred cccCCCCCcch-hHHHhHhhhhhccCCCcccccCccccc
Q 028361 44 CFPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 44 ~f~CP~C~e~~-d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
-|.||.|++-| ....|..|... |. ++--|..|..
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 47888888844 45678888877 44 4446666654
No 38
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=78.49 E-value=1 Score=29.65 Aligned_cols=29 Identities=24% Similarity=0.567 Sum_probs=18.3
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
+|.||-|+..|++... .....||-|..++
T Consensus 3 ~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEY-----------GTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCC-----------CCceECCCCCCeE
Confidence 5788888876665211 1156788887654
No 39
>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=77.28 E-value=1.1 Score=27.84 Aligned_cols=25 Identities=32% Similarity=0.814 Sum_probs=15.9
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
+.|+-||.-++... .+-+||+|...
T Consensus 2 ~~C~~CGy~y~~~~-------------~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE-------------APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc-------------CCCcCcCCCCc
Confidence 56888876444322 45588988663
No 40
>PRK12496 hypothetical protein; Provisional
Probab=76.97 E-value=0.91 Score=37.90 Aligned_cols=28 Identities=18% Similarity=0.445 Sum_probs=19.7
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchh
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 84 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~ 84 (210)
.+.||.|+..|+.. ..-.+||||...+.
T Consensus 127 ~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPED-------------YPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCC-------------CCCCcCCCCCChhh
Confidence 58899999877532 12248999977653
No 41
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=76.96 E-value=1.4 Score=31.68 Aligned_cols=25 Identities=24% Similarity=0.759 Sum_probs=20.5
Q ss_pred ccccCCCCCcch-hHHHhHhhhhhcc
Q 028361 43 ACFPCPFCYLEI-EAHMICSHLQEEH 67 (210)
Q Consensus 43 ~~f~CP~C~e~~-d~~~L~~H~~~eH 67 (210)
..+.|++|++.| +..+|..|+...|
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 369999999977 8999999998753
No 42
>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=76.29 E-value=0.57 Score=30.60 Aligned_cols=31 Identities=29% Similarity=0.477 Sum_probs=22.9
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCccccc
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
.+|.|+-|+..|++..-.. +...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~~~--------~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSIS--------EDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEcC--------CCCCCcCCCCCC
Confidence 5799999998887643211 246789999987
No 43
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=74.43 E-value=1.1 Score=34.94 Aligned_cols=38 Identities=18% Similarity=0.444 Sum_probs=23.0
Q ss_pred ccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhhh
Q 028361 41 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKD 86 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d 86 (210)
....|.||+|++ . .|-.=+ .+ ..--.+||+|-..-+..
T Consensus 18 lpt~f~CP~Cge-~---~v~v~~--~k--~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 18 LPKIFECPRCGK-V---SISVKI--KK--NIAIITCGNCGLYTEFE 55 (99)
T ss_pred CCcEeECCCCCC-e---Eeeeec--CC--CcceEECCCCCCccCEE
Confidence 457899999995 2 121111 11 13347899999876653
No 44
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=74.40 E-value=1.2 Score=30.02 Aligned_cols=46 Identities=30% Similarity=0.595 Sum_probs=30.2
Q ss_pred ccccCCC--CCcchhHHHhHhhhhhccCCCcccccCcc----cccchhh-hHHhh
Q 028361 43 ACFPCPF--CYLEIEAHMICSHLQEEHCFEMKNAVCPL----CAANLGK-DAAEH 90 (210)
Q Consensus 43 ~~f~CP~--C~e~~d~~~L~~H~~~eH~~e~~~~vCPv----C~~~v~~-d~i~H 90 (210)
...+||+ |.+.+-...|-.|+..+=+. +.+.||. |..++.+ ++..|
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~--~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPK--RPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTT--SEEE-SS----S--EEEHHHHHHC
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCC--CcEECCCCCCCCCCccchhHHhCC
Confidence 3578999 77789999999999864443 5678999 9988765 45544
No 45
>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=71.52 E-value=6 Score=28.30 Aligned_cols=38 Identities=21% Similarity=0.298 Sum_probs=24.4
Q ss_pred cccccCCCCCc------------chhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 42 KACFPCPFCYL------------EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 42 ~~~f~CP~C~e------------~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
+.+|.||.|++ -||...+-.++.. .+.+||+|...++.
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLSE 51 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-SG
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCCc
Confidence 45777887654 4677777777655 57899999888776
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=71.30 E-value=1.9 Score=27.08 Aligned_cols=26 Identities=31% Similarity=0.750 Sum_probs=17.0
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
.+.|+.||.-++... ..-+||||.+.
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 478999986544321 23499999874
No 47
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=71.07 E-value=1 Score=35.52 Aligned_cols=37 Identities=24% Similarity=0.500 Sum_probs=23.1
Q ss_pred ccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 41 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
+.-+|.||+|+..--++-+.. -...-.+++|-+|-..
T Consensus 19 L~k~FtCp~Cghe~vs~ctvk-----k~~~~g~~~Cg~CGls 55 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVK-----KTVNIGTAVCGNCGLS 55 (104)
T ss_pred CCceEecCccCCeeeeEEEEE-----ecCceeEEEcccCcce
Confidence 456899999987443332211 2333456789999765
No 48
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=70.57 E-value=3 Score=28.21 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=20.6
Q ss_pred ccCcccccchhh-hHHhhHhhhhcch
Q 028361 74 AVCPLCAANLGK-DAAEHFMVQHASS 98 (210)
Q Consensus 74 ~vCPvC~~~v~~-d~i~Hi~~qh~~~ 98 (210)
-.||.|.+.+.. .++.|+..+|..-
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHRSE 28 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCcCC
Confidence 479999997654 8999999999763
No 49
>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=70.14 E-value=1.9 Score=29.26 Aligned_cols=8 Identities=63% Similarity=1.393 Sum_probs=6.8
Q ss_pred ccCCCCCc
Q 028361 45 FPCPFCYL 52 (210)
Q Consensus 45 f~CP~C~e 52 (210)
-|||||+.
T Consensus 2 kPCPfCGg 9 (53)
T TIGR03655 2 KPCPFCGG 9 (53)
T ss_pred CCCCCCCC
Confidence 48999986
No 50
>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=69.78 E-value=3 Score=35.07 Aligned_cols=54 Identities=24% Similarity=0.438 Sum_probs=32.5
Q ss_pred ccccCCC----CCcchhHHHhHhhhhhccCCCcccccCcc----cccc-hhhhHHhhHhhhhcchh
Q 028361 43 ACFPCPF----CYLEIEAHMICSHLQEEHCFEMKNAVCPL----CAAN-LGKDAAEHFMVQHASSL 99 (210)
Q Consensus 43 ~~f~CP~----C~e~~d~~~L~~H~~~eH~~e~~~~vCPv----C~~~-v~~d~i~Hi~~qh~~~~ 99 (210)
-.|||+| |.+.+-......|.+. -.+ ++-.||+ |.-. ...++..|++..|+...
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 4799999 9999999999999644 444 3456998 6432 44599999999998844
No 51
>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=69.70 E-value=1.9 Score=32.19 Aligned_cols=35 Identities=20% Similarity=0.617 Sum_probs=13.4
Q ss_pred ccccccCCCCC-c-chhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 41 VKACFPCPFCY-L-EIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 41 ~~~~f~CP~C~-e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
+...|.||||+ + -+.+.- +.....-.+.|-+|...
T Consensus 19 l~~~F~CPfC~~~~sV~v~i-------dkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVKI-------DKKEGIGILSCRVCGES 55 (81)
T ss_dssp -SS----TTT--SS-EEEEE-------ETTTTEEEEEESSS--E
T ss_pred CCceEcCCcCCCCCeEEEEE-------EccCCEEEEEecCCCCe
Confidence 45789999998 3 222211 11122334669999664
No 52
>PF12773 DZR: Double zinc ribbon
Probab=69.61 E-value=2.3 Score=27.97 Aligned_cols=28 Identities=25% Similarity=0.569 Sum_probs=17.5
Q ss_pred cCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 46 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 46 ~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
-||.|+..+. ..+....+||.|...+..
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAENPP 41 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCCCcC
Confidence 3666666554 334556788888876554
No 53
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=67.85 E-value=2.9 Score=24.77 Aligned_cols=12 Identities=42% Similarity=0.977 Sum_probs=10.0
Q ss_pred ccccccCCCCCc
Q 028361 41 VKACFPCPFCYL 52 (210)
Q Consensus 41 ~~~~f~CP~C~e 52 (210)
.-..|+||-||+
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 456899999986
No 54
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.10 E-value=4.1 Score=34.49 Aligned_cols=36 Identities=22% Similarity=0.489 Sum_probs=25.1
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
.....|.||-|+.-|....-.. ..-.||+|...+-.
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEMLEE 148 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCCee
Confidence 4568999999997444433221 35699999998754
No 55
>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=67.09 E-value=4 Score=33.76 Aligned_cols=37 Identities=24% Similarity=0.432 Sum_probs=26.2
Q ss_pred ccccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 39 ~d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
+.....|.||-|+.-|....-.. .+-.||+|...+-.
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAMLDY 140 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEeee
Confidence 34678899999997554444443 26799999998643
No 56
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=66.44 E-value=3 Score=28.28 Aligned_cols=20 Identities=25% Similarity=0.743 Sum_probs=9.8
Q ss_pred ccCcccccchhh----hHHhhHhh
Q 028361 74 AVCPLCAANLGK----DAAEHFMV 93 (210)
Q Consensus 74 ~vCPvC~~~v~~----d~i~Hi~~ 93 (210)
++||||...++. ++|.+++.
T Consensus 21 ~~CPlC~r~l~~e~~~~li~~~~~ 44 (54)
T PF04423_consen 21 GCCPLCGRPLDEEHRQELIKKYKS 44 (54)
T ss_dssp EE-TTT--EE-HHHHHHHHHHHHH
T ss_pred CcCCCCCCCCCHHHHHHHHHHHHH
Confidence 378888777765 45555553
No 57
>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=66.27 E-value=1.8 Score=25.28 Aligned_cols=10 Identities=30% Similarity=1.175 Sum_probs=8.6
Q ss_pred ccCCCCCcch
Q 028361 45 FPCPFCYLEI 54 (210)
Q Consensus 45 f~CP~C~e~~ 54 (210)
|+||+|+..|
T Consensus 15 ~~C~~C~k~F 24 (26)
T PF13465_consen 15 YKCPYCGKSF 24 (26)
T ss_dssp EEESSSSEEE
T ss_pred CCCCCCcCee
Confidence 9999998755
No 58
>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=66.10 E-value=0.96 Score=33.30 Aligned_cols=39 Identities=31% Similarity=0.403 Sum_probs=20.9
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
..||-|..+++..+-.-||+.=+..=.+.+.||-|...+
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~L 40 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPL 40 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHH
Confidence 468888877777775444443333334568899999875
No 59
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.97 E-value=2.2 Score=38.34 Aligned_cols=40 Identities=23% Similarity=0.553 Sum_probs=22.2
Q ss_pred cccccCCCCCcchhHHHhH--------hhhh------hccCCCcccccCccccc
Q 028361 42 KACFPCPFCYLEIEAHMIC--------SHLQ------EEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 42 ~~~f~CP~C~e~~d~~~L~--------~H~~------~eH~~e~~~~vCPvC~~ 81 (210)
..++.||+|+.-|--.... --++ +--|+=-..+|||+|--
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~y 70 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYY 70 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhH
Confidence 3579999998655332211 1111 22233334588999964
No 60
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.37 E-value=2.7 Score=40.49 Aligned_cols=43 Identities=28% Similarity=0.458 Sum_probs=28.7
Q ss_pred ccccCccccccccCCCCCc---chhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 34 ETEIDDDVKACFPCPFCYL---EIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 34 ~~~~d~d~~~~f~CP~C~e---~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
+.+.++..+..|.||+|.. .+|+..|.. ++...-.|-.|..-|
T Consensus 118 d~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~-------~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 118 DRLRDDTNVAGYVCPNCQKKYTSLEALQLLD-------NETGEFHCENCGGEL 163 (436)
T ss_pred HHhhhccccccccCCccccchhhhHHHHhhc-------ccCceEEEecCCCch
Confidence 3445566899999999987 555555554 223445788887654
No 61
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=64.56 E-value=3.8 Score=42.23 Aligned_cols=41 Identities=22% Similarity=0.472 Sum_probs=35.5
Q ss_pred cccccCCCCCcch-hHHHhHhhhhhccCCCcccccCcccccc
Q 028361 42 KACFPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 42 ~~~f~CP~C~e~~-d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
-+..+||||..++ -...|..|+.-.|--..-|--|+.|...
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsyt 249 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYT 249 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhh
Confidence 3457999999855 5689999999999999999999999986
No 62
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=64.00 E-value=3.1 Score=29.78 Aligned_cols=17 Identities=24% Similarity=0.165 Sum_probs=14.5
Q ss_pred hhhHHhhHhhhhcchhh
Q 028361 84 GKDAAEHFMVQHASSLK 100 (210)
Q Consensus 84 ~~d~i~Hi~~qh~~~~K 100 (210)
.+|.++|++--|+.+|-
T Consensus 30 ~K~Y~RHVNKaH~~~~~ 46 (65)
T COG4049 30 RKDYIRHVNKAHGWLFG 46 (65)
T ss_pred hHHHHHHhhHHhhhhhc
Confidence 45889999999999984
No 63
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=63.72 E-value=1.9 Score=33.16 Aligned_cols=15 Identities=33% Similarity=0.687 Sum_probs=12.3
Q ss_pred CccccccccCCCCCc
Q 028361 38 DDDVKACFPCPFCYL 52 (210)
Q Consensus 38 d~d~~~~f~CP~C~e 52 (210)
|..+...|.||||+.
T Consensus 30 e~~q~a~y~CpfCgk 44 (90)
T PTZ00255 30 EISQHAKYFCPFCGK 44 (90)
T ss_pred HHHHhCCccCCCCCC
Confidence 345789999999986
No 64
>PRK12495 hypothetical protein; Provisional
Probab=63.39 E-value=3.6 Score=36.51 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=23.6
Q ss_pred cccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 42 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 42 ~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
...|-||.|+..|- .+ ....+||+|-..+..
T Consensus 40 msa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 40 MTNAHCDECGDPIF------------RH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred cchhhcccccCccc------------CC-CCeeECCCCCCcccc
Confidence 45789999998665 22 445789999998875
No 65
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=62.39 E-value=4.7 Score=34.15 Aligned_cols=25 Identities=36% Similarity=0.822 Sum_probs=17.3
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
.+.||-||.- |-. --+.+||||.+.
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 8999999641 111 335799999864
No 66
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=61.80 E-value=6.1 Score=28.40 Aligned_cols=35 Identities=34% Similarity=0.689 Sum_probs=22.3
Q ss_pred ccccccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccc
Q 028361 39 DDVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCA 80 (210)
Q Consensus 39 ~d~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~ 80 (210)
+|--..|+||-|++ .|=.-.-|.-+ .+.-+||-|-
T Consensus 22 ~e~~v~F~CPnCGe~~I~Rc~~CRk~-------g~~Y~Cp~CG 57 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYRCAKCRKL-------GNPYRCPKCG 57 (61)
T ss_pred CCceeEeeCCCCCceeeehhhhHHHc-------CCceECCCcC
Confidence 34567899999996 55544444322 2344898884
No 67
>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=60.77 E-value=4.4 Score=25.96 Aligned_cols=28 Identities=25% Similarity=0.407 Sum_probs=14.5
Q ss_pred cccccccCCCCCcchhH-----HHhHhhhhhcc
Q 028361 40 DVKACFPCPFCYLEIEA-----HMICSHLQEEH 67 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~-----~~L~~H~~~eH 67 (210)
.......|-||+..+.. ..|..|+..-|
T Consensus 12 ~~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 12 GDKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp GCSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CCcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 34556677777765544 36666665444
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=59.60 E-value=3.8 Score=32.62 Aligned_cols=26 Identities=31% Similarity=0.718 Sum_probs=16.8
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
-+||-|..+|.- -+....|||-|+.-
T Consensus 3 p~CP~C~seytY------------~dg~~~iCpeC~~E 28 (109)
T TIGR00686 3 PPCPKCNSEYTY------------HDGTQLICPSCLYE 28 (109)
T ss_pred CcCCcCCCcceE------------ecCCeeECcccccc
Confidence 368888765432 13345799999864
No 69
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=59.54 E-value=5.5 Score=23.75 Aligned_cols=9 Identities=44% Similarity=1.047 Sum_probs=5.1
Q ss_pred cCCCCCcch
Q 028361 46 PCPFCYLEI 54 (210)
Q Consensus 46 ~CP~C~e~~ 54 (210)
.||-|+..+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 366666554
No 70
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=59.42 E-value=4.1 Score=31.75 Aligned_cols=9 Identities=44% Similarity=1.331 Sum_probs=7.7
Q ss_pred cccCCCCCc
Q 028361 44 CFPCPFCYL 52 (210)
Q Consensus 44 ~f~CP~C~e 52 (210)
-++||||++
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 478999997
No 71
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=59.32 E-value=5.8 Score=23.24 Aligned_cols=23 Identities=39% Similarity=0.857 Sum_probs=14.3
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
..||.|+..++ .....||.|-.+
T Consensus 3 ~~Cp~Cg~~~~---------------~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEID---------------PDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCC---------------cccccChhhCCC
Confidence 46888887442 224567777654
No 72
>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=58.79 E-value=2.6 Score=35.70 Aligned_cols=42 Identities=21% Similarity=0.418 Sum_probs=21.3
Q ss_pred cccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 42 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 42 ~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
+-.|+||.|+..+...++.. .+.-.....-..||-|......
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~~~ 57 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPLSP 57 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B--H
T ss_pred ceEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcCCH
Confidence 46899999999888888665 1111223345779999997654
No 73
>PF13395 HNH_4: HNH endonuclease
Probab=58.23 E-value=5 Score=27.27 Aligned_cols=14 Identities=29% Similarity=0.778 Sum_probs=12.0
Q ss_pred CCCCCcchhHHHhH
Q 028361 47 CPFCYLEIEAHMIC 60 (210)
Q Consensus 47 CP~C~e~~d~~~L~ 60 (210)
||||++.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999988763
No 74
>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=57.39 E-value=4.2 Score=31.96 Aligned_cols=30 Identities=23% Similarity=0.399 Sum_probs=23.1
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
+.+..+.|+-|+..|.+... ...||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 46788999999987776533 3579999864
No 75
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=57.14 E-value=5.5 Score=26.54 Aligned_cols=26 Identities=19% Similarity=0.433 Sum_probs=18.9
Q ss_pred ccccCCCCCcchhHH------HhHhhhhhccC
Q 028361 43 ACFPCPFCYLEIEAH------MICSHLQEEHC 68 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~------~L~~H~~~eH~ 68 (210)
+...|-+|+..|... .|..|+..-||
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 678899998866554 67777776555
No 76
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=57.12 E-value=2.8 Score=32.35 Aligned_cols=15 Identities=40% Similarity=0.798 Sum_probs=12.1
Q ss_pred CccccccccCCCCCc
Q 028361 38 DDDVKACFPCPFCYL 52 (210)
Q Consensus 38 d~d~~~~f~CP~C~e 52 (210)
+..+...|.||||+.
T Consensus 29 e~~q~a~y~CpfCgk 43 (91)
T TIGR00280 29 EIQQKAKYVCPFCGK 43 (91)
T ss_pred HHHHhcCccCCCCCC
Confidence 345788999999975
No 77
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.03 E-value=5.1 Score=26.66 Aligned_cols=28 Identities=21% Similarity=0.392 Sum_probs=19.8
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
.|.|.-|+.++++. ....+.||-|..+|
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 47888898877754 23457899987553
No 78
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=57.00 E-value=3.7 Score=23.72 Aligned_cols=8 Identities=63% Similarity=1.244 Sum_probs=4.7
Q ss_pred CCCCCcch
Q 028361 47 CPFCYLEI 54 (210)
Q Consensus 47 CP~C~e~~ 54 (210)
||.|+..+
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 66666543
No 79
>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=56.94 E-value=6 Score=25.00 Aligned_cols=23 Identities=26% Similarity=0.560 Sum_probs=13.2
Q ss_pred ccccCCCCCcchhHHHhHhhhhh
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQE 65 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~ 65 (210)
.+|.||-|+..+-..-+--|++.
T Consensus 3 ~~~~C~nC~R~v~a~RfA~HLek 25 (33)
T PF08209_consen 3 PYVECPNCGRPVAASRFAPHLEK 25 (33)
T ss_dssp -EEE-TTTSSEEEGGGHHHHHHH
T ss_pred CeEECCCCcCCcchhhhHHHHHH
Confidence 35666666666666666666653
No 80
>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=56.86 E-value=11 Score=26.35 Aligned_cols=42 Identities=17% Similarity=0.310 Sum_probs=30.8
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhhhHHhhHh
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHFM 92 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d~i~Hi~ 92 (210)
+....=.||.|+.-... ....+..+||.|.....+|..+=++
T Consensus 24 ~~~TSq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~rD~naA~N 65 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMDRDVNAARN 65 (69)
T ss_pred CCCCccCccCccccccc-----------ccccceEEcCCCCCEECcHHHHHHH
Confidence 44477889999873322 4556678999999999998876554
No 81
>smart00355 ZnF_C2H2 zinc finger.
Probab=56.66 E-value=9.1 Score=20.42 Aligned_cols=20 Identities=20% Similarity=0.504 Sum_probs=12.0
Q ss_pred ccCCCCCcc-hhHHHhHhhhh
Q 028361 45 FPCPFCYLE-IEAHMICSHLQ 64 (210)
Q Consensus 45 f~CP~C~e~-~d~~~L~~H~~ 64 (210)
|.|+.|+.. -....|..|+.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH
Confidence 467777763 34456666665
No 82
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=56.59 E-value=2.8 Score=39.76 Aligned_cols=15 Identities=27% Similarity=0.640 Sum_probs=11.7
Q ss_pred CcccccCcccccchh
Q 028361 70 EMKNAVCPLCAANLG 84 (210)
Q Consensus 70 e~~~~vCPvC~~~v~ 84 (210)
+.-||-||.|..+-.
T Consensus 50 q~lngrcpacrr~y~ 64 (480)
T COG5175 50 QNLNGRCPACRRKYD 64 (480)
T ss_pred hhccCCChHhhhhcc
Confidence 347999999988743
No 83
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=56.58 E-value=7 Score=26.24 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=4.2
Q ss_pred Ccccccchh
Q 028361 76 CPLCAANLG 84 (210)
Q Consensus 76 CPvC~~~v~ 84 (210)
||-|..+-+
T Consensus 1 CP~C~~kkk 9 (43)
T PF03470_consen 1 CPFCPGKKK 9 (43)
T ss_pred CCCCCCCCC
Confidence 444444443
No 84
>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=56.55 E-value=7 Score=26.75 Aligned_cols=13 Identities=31% Similarity=0.761 Sum_probs=9.5
Q ss_pred cccccccCCCCCc
Q 028361 40 DVKACFPCPFCYL 52 (210)
Q Consensus 40 d~~~~f~CP~C~e 52 (210)
+++.+|.||-|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (50)
T cd00730 30 DLPDDWVCPVCGA 42 (50)
T ss_pred HCCCCCCCCCCCC
Confidence 4677788888865
No 85
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=56.04 E-value=3.1 Score=32.06 Aligned_cols=15 Identities=27% Similarity=0.720 Sum_probs=12.0
Q ss_pred CccccccccCCCCCc
Q 028361 38 DDDVKACFPCPFCYL 52 (210)
Q Consensus 38 d~d~~~~f~CP~C~e 52 (210)
+..+.+.|.||||+.
T Consensus 30 e~~q~a~y~CpfCgk 44 (90)
T PRK03976 30 EEKMRAKHVCPVCGR 44 (90)
T ss_pred HHHHhcCccCCCCCC
Confidence 345788999999975
No 86
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=55.85 E-value=5.1 Score=38.53 Aligned_cols=34 Identities=32% Similarity=0.836 Sum_probs=17.2
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCccccc-chhhhHHh
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA-NLGKDAAE 89 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~-~v~~d~i~ 89 (210)
+...||||+.-|. | +-+.-+||||-- .||.+.+|
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 5678999987542 2 245679999976 47877654
No 87
>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=55.53 E-value=3.4 Score=32.25 Aligned_cols=30 Identities=30% Similarity=0.492 Sum_probs=20.1
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
..+..+.|+-|+..|++..... .||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~-------------~CP~Cgs~ 95 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFDF-------------SCPRCGSP 95 (113)
T ss_dssp EE--EEEETTTS-EEECHHCCH-------------H-SSSSSS
T ss_pred ecCCcEECCCCCCEEecCCCCC-------------CCcCCcCC
Confidence 4678999999999888765542 39999875
No 88
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.20 E-value=5.4 Score=32.22 Aligned_cols=43 Identities=26% Similarity=0.451 Sum_probs=24.8
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhc-----cCCC---cccccCcccccc
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEE-----HCFE---MKNAVCPLCAAN 82 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~e-----H~~e---~~~~vCPvC~~~ 82 (210)
..+..+.|+-|+..+.+..-..+++.+ |-.. .....||.|...
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 467899999999876654211211111 1111 234679999864
No 89
>smart00507 HNHc HNH nucleases.
Probab=55.19 E-value=2.8 Score=26.34 Aligned_cols=21 Identities=14% Similarity=0.316 Sum_probs=14.2
Q ss_pred ccCCCCCcchhHHHhHhhhhh
Q 028361 45 FPCPFCYLEIEAHMICSHLQE 65 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~ 65 (210)
+.|+||+..++...-++|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 799999987764334555553
No 90
>PRK00420 hypothetical protein; Validated
Probab=54.51 E-value=7.7 Score=30.89 Aligned_cols=27 Identities=26% Similarity=0.550 Sum_probs=17.9
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
-.||.|+..+= .| .....+||+|..-+
T Consensus 24 ~~CP~Cg~pLf--~l----------k~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLF--EL----------KDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcce--ec----------CCCceECCCCCCee
Confidence 68999986431 11 13457999999864
No 91
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=54.25 E-value=9 Score=27.38 Aligned_cols=34 Identities=26% Similarity=0.614 Sum_probs=22.3
Q ss_pred cccccccCCCCCcc-hhHHHhHhhhhhccCCCcccccCcccc
Q 028361 40 DVKACFPCPFCYLE-IEAHMICSHLQEEHCFEMKNAVCPLCA 80 (210)
Q Consensus 40 d~~~~f~CP~C~e~-~d~~~L~~H~~~eH~~e~~~~vCPvC~ 80 (210)
+.-..|.||-|++. +=. |..+-. .+..-+||-|-
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 34678999999985 544 443322 24556899885
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=53.84 E-value=6.3 Score=26.69 Aligned_cols=14 Identities=29% Similarity=0.771 Sum_probs=8.7
Q ss_pred ccccccccCCCCCc
Q 028361 39 DDVKACFPCPFCYL 52 (210)
Q Consensus 39 ~d~~~~f~CP~C~e 52 (210)
++++..+.||-|+.
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 46788899999975
No 93
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=52.71 E-value=6.9 Score=39.20 Aligned_cols=56 Identities=29% Similarity=0.484 Sum_probs=37.4
Q ss_pred cCccccccccCCCCCc--chhHHHhHhhh-----h---hccCCCcccccCcccccchhhhHHhhHh
Q 028361 37 IDDDVKACFPCPFCYL--EIEAHMICSHL-----Q---EEHCFEMKNAVCPLCAANLGKDAAEHFM 92 (210)
Q Consensus 37 ~d~d~~~~f~CP~C~e--~~d~~~L~~H~-----~---~eH~~e~~~~vCPvC~~~v~~d~i~Hi~ 92 (210)
.++|+..+..|-+|.. +==+.+=|.|. - -+--.+..|+.||+|...++-|+-.|--
T Consensus 529 ~~~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~al 594 (791)
T KOG1002|consen 529 LPDENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPAL 594 (791)
T ss_pred CCccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchhh
Confidence 4567888999999976 22233334432 1 1234477889999999998888766643
No 94
>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=51.32 E-value=6.8 Score=38.54 Aligned_cols=43 Identities=23% Similarity=0.478 Sum_probs=28.1
Q ss_pred cccccCCCCCcchhHH--HhHhhhhhccCCCcccccCcccccchhhh
Q 028361 42 KACFPCPFCYLEIEAH--MICSHLQEEHCFEMKNAVCPLCAANLGKD 86 (210)
Q Consensus 42 ~~~f~CP~C~e~~d~~--~L~~H~~~eH~~e~~~~vCPvC~~~v~~d 86 (210)
+...+||-|++.+... .|.- +++...+.--.+||-|...+...
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w--~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKW--DKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred EEEccCCCCCCCccccccceee--cCCCCccceEEECCCCcCCCCHH
Confidence 6789999999855543 3322 22223444457899999998764
No 95
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=51.17 E-value=5.9 Score=31.05 Aligned_cols=31 Identities=29% Similarity=0.396 Sum_probs=22.3
Q ss_pred ccccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 39 ~d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
++.+..+.|+-|+..|.+.. ....||.|...
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred EeeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 34678999999997666543 23469999864
No 96
>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=50.44 E-value=7.2 Score=30.56 Aligned_cols=39 Identities=28% Similarity=0.458 Sum_probs=22.2
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCc-c-cccCcccccchhh
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEM-K-NAVCPLCAANLGK 85 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~-~-~~vCPvC~~~v~~ 85 (210)
..||||+....++.= +-+=- |.++. . .-+|+-|.+.||.
T Consensus 3 ~~CpYCg~~~~l~~~-~~iYg-~~~~~~~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELVDG-SEIYG-HRYDDGPYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEccc-chhcC-ccCCCCceeEECCCCCceeee
Confidence 479999985444331 10101 22211 1 2689999999885
No 97
>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=50.23 E-value=2.2 Score=27.18 Aligned_cols=37 Identities=19% Similarity=0.504 Sum_probs=15.3
Q ss_pred CCCCCcchhHH--HhHhhhhhcc---CCCccc--ccCcccccch
Q 028361 47 CPFCYLEIEAH--MICSHLQEEH---CFEMKN--AVCPLCAANL 83 (210)
Q Consensus 47 CP~C~e~~d~~--~L~~H~~~eH---~~e~~~--~vCPvC~~~v 83 (210)
|++|++.+... .-++|+.... .++..| .+|+.|....
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~~k 44 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHRKK 44 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHHHH
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHHHh
Confidence 89998876665 2344443322 223333 4577775543
No 98
>PRK03922 hypothetical protein; Provisional
Probab=50.01 E-value=7.2 Score=31.20 Aligned_cols=15 Identities=20% Similarity=0.430 Sum_probs=12.0
Q ss_pred cccCCCCCcchhHHH
Q 028361 44 CFPCPFCYLEIEAHM 58 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~ 58 (210)
.-.||+|+++||-..
T Consensus 49 ~~~cP~cge~~~~af 63 (113)
T PRK03922 49 LTICPKCGEPFDSAF 63 (113)
T ss_pred cccCCCCCCcCCcEE
Confidence 468999999998543
No 99
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=50.00 E-value=12 Score=32.19 Aligned_cols=38 Identities=18% Similarity=0.352 Sum_probs=29.8
Q ss_pred ccccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhhhHHhhHh
Q 028361 39 DDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHFM 92 (210)
Q Consensus 39 ~d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d~i~Hi~ 92 (210)
++....-.||.||. ...+...||.|....-+|..+=++
T Consensus 304 ~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~N 341 (364)
T COG0675 304 PPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALN 341 (364)
T ss_pred CCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHHH
Confidence 34455688999998 335678999999999898887776
No 100
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.74 E-value=8.4 Score=36.80 Aligned_cols=13 Identities=46% Similarity=1.081 Sum_probs=10.1
Q ss_pred cccCCCCCcchhH
Q 028361 44 CFPCPFCYLEIEA 56 (210)
Q Consensus 44 ~f~CP~C~e~~d~ 56 (210)
.|+||||..+-+.
T Consensus 374 sfKCPYCP~e~~~ 386 (394)
T KOG2817|consen 374 SFKCPYCPVEQLA 386 (394)
T ss_pred eeeCCCCCcccCH
Confidence 5999999876543
No 101
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=48.48 E-value=7.8 Score=30.47 Aligned_cols=15 Identities=27% Similarity=0.523 Sum_probs=11.9
Q ss_pred cccCCCCCcchhHHH
Q 028361 44 CFPCPFCYLEIEAHM 58 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~ 58 (210)
...||+|+++|+-..
T Consensus 47 ~~~cP~Cge~~~~a~ 61 (102)
T PF04475_consen 47 DTICPKCGEELDSAF 61 (102)
T ss_pred cccCCCCCCccCceE
Confidence 468999999988543
No 102
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=48.02 E-value=11 Score=21.40 Aligned_cols=21 Identities=19% Similarity=0.385 Sum_probs=13.4
Q ss_pred ccCCCCCcch-hHHHhHhhhhh
Q 028361 45 FPCPFCYLEI-EAHMICSHLQE 65 (210)
Q Consensus 45 f~CP~C~e~~-d~~~L~~H~~~ 65 (210)
|.|..|+..| +...|..|...
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~ 23 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRS 23 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCT
T ss_pred CCCCccCCccCChhHHHHHhHH
Confidence 6677777733 46667777644
No 103
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=46.63 E-value=15 Score=23.62 Aligned_cols=10 Identities=40% Similarity=1.059 Sum_probs=7.7
Q ss_pred cccccCcccc
Q 028361 71 MKNAVCPLCA 80 (210)
Q Consensus 71 ~~~~vCPvC~ 80 (210)
.+..+||+|.
T Consensus 34 ~~~~~CP~C~ 43 (44)
T PF14634_consen 34 GKSVKCPICR 43 (44)
T ss_pred CCCCCCcCCC
Confidence 5668899985
No 104
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=46.41 E-value=8.5 Score=36.20 Aligned_cols=10 Identities=40% Similarity=1.142 Sum_probs=8.5
Q ss_pred cccCCCCCcc
Q 028361 44 CFPCPFCYLE 53 (210)
Q Consensus 44 ~f~CP~C~e~ 53 (210)
.|+||||.++
T Consensus 376 ~FKCPYCP~~ 385 (396)
T COG5109 376 SFKCPYCPEM 385 (396)
T ss_pred EeeCCCCCcc
Confidence 6999999873
No 105
>PHA00616 hypothetical protein
Probab=46.30 E-value=12 Score=25.11 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=10.0
Q ss_pred ccCCCCCc-chhHHHhHhhhhh
Q 028361 45 FPCPFCYL-EIEAHMICSHLQE 65 (210)
Q Consensus 45 f~CP~C~e-~~d~~~L~~H~~~ 65 (210)
|.||-||. =..-..|..|+..
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~ 23 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLS 23 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHH
Confidence 45666655 3334444444433
No 106
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=45.94 E-value=11 Score=23.80 Aligned_cols=31 Identities=19% Similarity=0.378 Sum_probs=18.2
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCccccc
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
..||-|...|.+..=. =+...+.+-||.|..
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 5688887755554311 123355677888864
No 107
>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=45.51 E-value=11 Score=34.83 Aligned_cols=40 Identities=28% Similarity=0.566 Sum_probs=24.8
Q ss_pred ccCCCCCc----chhH--------HHhHhhhhhccCCCcccccCcccccchhh
Q 028361 45 FPCPFCYL----EIEA--------HMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 45 f~CP~C~e----~~d~--------~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
+.||.|.. +=+. ..+|..|-+.. +....+.||+|...+..
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l-~~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLL-FVRGSGSCPECDTPLRK 55 (309)
T ss_pred CCCCcCCCCCccCcccccccCCCCCcccHHHHHHH-hcCCCCCCCCCCCccch
Confidence 68999976 2221 12455566654 33345789999887654
No 108
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=45.26 E-value=11 Score=35.70 Aligned_cols=41 Identities=20% Similarity=0.386 Sum_probs=30.9
Q ss_pred ccccCCC--CCc-chhHHHhHhhhhhccCC-----------------CcccccCcccccch
Q 028361 43 ACFPCPF--CYL-EIEAHMICSHLQEEHCF-----------------EMKNAVCPLCAANL 83 (210)
Q Consensus 43 ~~f~CP~--C~e-~~d~~~L~~H~~~eH~~-----------------e~~~~vCPvC~~~v 83 (210)
--|+||. |.+ .-.+-||--|.-.-|+. +.|+-+|+||.++-
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 3488885 877 66788999998888832 33667899999874
No 109
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=44.86 E-value=11 Score=31.07 Aligned_cols=40 Identities=28% Similarity=0.480 Sum_probs=29.1
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhhhH
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDA 87 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d~ 87 (210)
..+.|..|+..++...+...+..... ..||.|...+--|+
T Consensus 104 ~~~~C~~C~~~~~~~~~~~~~~~~~~-----~~C~~C~~~lrp~v 143 (178)
T PF02146_consen 104 FRLRCSKCGKEYDREDIVDSIDEEEP-----PRCPKCGGLLRPDV 143 (178)
T ss_dssp EEEEETTTSBEEEGHHHHHHHHTTSS-----CBCTTTSCBEEEEE
T ss_pred ceeeecCCCccccchhhccccccccc-----ccccccCccCCCCe
Confidence 46899999998888777766555332 39999999755443
No 110
>PRK10220 hypothetical protein; Provisional
Probab=44.11 E-value=12 Score=29.94 Aligned_cols=25 Identities=36% Similarity=0.748 Sum_probs=15.7
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCC-cccccCcccccc
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFE-MKNAVCPLCAAN 82 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e-~~~~vCPvC~~~ 82 (210)
-+||-|..+|. |+ ...-|||-|+.-
T Consensus 4 P~CP~C~seyt-------------Y~d~~~~vCpeC~hE 29 (111)
T PRK10220 4 PHCPKCNSEYT-------------YEDNGMYICPECAHE 29 (111)
T ss_pred CcCCCCCCcce-------------EcCCCeEECCcccCc
Confidence 36888865442 22 334789999764
No 111
>PRK11595 DNA utilization protein GntX; Provisional
Probab=43.82 E-value=13 Score=32.13 Aligned_cols=35 Identities=23% Similarity=0.477 Sum_probs=22.9
Q ss_pred cCCCCCcchhH--HHhHhhhhhccCCCcccccCcccccc
Q 028361 46 PCPFCYLEIEA--HMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 46 ~CP~C~e~~d~--~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
.|+.|+..+.. ..||.+|.+.=++- ...||.|...
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 48999876543 35888887654331 3478888754
No 112
>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=43.80 E-value=11 Score=29.58 Aligned_cols=34 Identities=21% Similarity=0.516 Sum_probs=23.7
Q ss_pred cccccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccchhhh
Q 028361 40 DVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKD 86 (210)
Q Consensus 40 d~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d 86 (210)
|+-....||-||. =||..- .++|||-|..-.-..
T Consensus 5 elGtKR~Cp~CG~kFYDLnk-------------~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDLNK-------------DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCcccCCCCcchhccCCC-------------CCccCCCCCCccCcc
Confidence 4556778999987 666662 356899998876544
No 113
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=43.71 E-value=7.6 Score=33.95 Aligned_cols=32 Identities=19% Similarity=0.438 Sum_probs=20.9
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCC-ccccc
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFE-MKNAV 75 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e-~~~~v 75 (210)
.|.||.|...+.+..=--+|+..|.|| +|.|.
T Consensus 2 ~~~CP~C~~~l~~~~~~~~C~~~h~fd~a~~Gy 34 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSWICPQNHQFDCAKEGY 34 (272)
T ss_pred cccCCCCCcchhcCCCEEEcCCCCCCccccCce
Confidence 489999999775332223456789995 45554
No 114
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=43.58 E-value=18 Score=39.37 Aligned_cols=41 Identities=24% Similarity=0.506 Sum_probs=26.5
Q ss_pred cccccccCCCCC-cchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 40 DVKACFPCPFCY-LEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 40 d~~~~f~CP~C~-e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
-+++-|.||-|- .+|--.+= ..--||.-.-.||.|...+.+
T Consensus 910 PL~PHY~Cp~Cky~Ef~~d~s-----vgsGfDLpdK~CPkCg~pl~k 951 (1444)
T COG2176 910 PLPPHYLCPECKYSEFIDDGS-----VGSGFDLPDKDCPKCGTPLKK 951 (1444)
T ss_pred CCCccccCCCCceeeeecCCC-----cCCCCCCCCCCCCcCCCcccc
Confidence 478999999993 34422111 113566667789999998543
No 115
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=42.89 E-value=13 Score=23.50 Aligned_cols=31 Identities=19% Similarity=0.346 Sum_probs=18.5
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCcccccCccccc
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
+.||-|...|++..-. =|-....+-||.|..
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 5688887765554321 244455677887754
No 116
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.31 E-value=11 Score=27.28 Aligned_cols=13 Identities=23% Similarity=0.748 Sum_probs=9.6
Q ss_pred cccccCCCCCcch
Q 028361 42 KACFPCPFCYLEI 54 (210)
Q Consensus 42 ~~~f~CP~C~e~~ 54 (210)
.-+..||||+.-|
T Consensus 46 ~gev~CPYC~t~y 58 (62)
T COG4391 46 EGEVVCPYCSTRY 58 (62)
T ss_pred CCcEecCccccEE
Confidence 3578999998643
No 117
>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=41.75 E-value=11 Score=29.01 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=10.7
Q ss_pred ccccccccCCCCCc
Q 028361 39 DDVKACFPCPFCYL 52 (210)
Q Consensus 39 ~d~~~~f~CP~C~e 52 (210)
..+...|.||||+.
T Consensus 30 ~~q~~ky~Cp~Cgk 43 (90)
T PF01780_consen 30 ISQHAKYTCPFCGK 43 (90)
T ss_dssp HHHHS-BEESSSSS
T ss_pred HHHhCCCcCCCCCC
Confidence 44678999999987
No 118
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=40.81 E-value=20 Score=33.79 Aligned_cols=28 Identities=32% Similarity=0.743 Sum_probs=23.2
Q ss_pred cccCcccccchh--------------------------hhHHhhHhhhhcchhh
Q 028361 73 NAVCPLCAANLG--------------------------KDAAEHFMVQHASSLK 100 (210)
Q Consensus 73 ~~vCPvC~~~v~--------------------------~d~i~Hi~~qh~~~~K 100 (210)
-.+||.|..+|- +|+-+||+-.|+.++|
T Consensus 123 dK~Cp~C~d~VqrIeq~~~g~iFmC~~~~GC~RTyLsqrDlqAHInhrH~~~~~ 176 (389)
T KOG2932|consen 123 DKICPLCDDRVQRIEQIMMGGIFMCAAPHGCLRTYLSQRDLQAHINHRHGSLLQ 176 (389)
T ss_pred cccCcCcccHHHHHHHhcccceEEeecchhHHHHHhhHHHHHHHhhhhhccccC
Confidence 358999999852 3999999988998887
No 119
>PRK12860 transcriptional activator FlhC; Provisional
Probab=40.69 E-value=20 Score=31.00 Aligned_cols=31 Identities=26% Similarity=0.510 Sum_probs=21.3
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCc-ccccCcccc
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEM-KNAVCPLCA 80 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~-~~~vCPvC~ 80 (210)
++...-+|..|+-.|= . |..|. .+.+||+|.
T Consensus 130 ~~L~l~~C~~Cgg~fv-----~-----~~~e~~~~f~CplC~ 161 (189)
T PRK12860 130 GMLQLARCCRCGGKFV-----T-----HAHDLRHNFVCGLCQ 161 (189)
T ss_pred CCeeeccCCCCCCCee-----c-----cccccCCCCcCCCCC
Confidence 4667889999987552 1 23343 457999997
No 120
>PHA02929 N1R/p28-like protein; Provisional
Probab=40.44 E-value=6.2 Score=35.15 Aligned_cols=45 Identities=18% Similarity=0.499 Sum_probs=25.9
Q ss_pred cccccccCCCCCcchhHH----------HhHhhhhhccCC---CcccccCcccccchh
Q 028361 40 DVKACFPCPFCYLEIEAH----------MICSHLQEEHCF---EMKNAVCPLCAANLG 84 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~----------~L~~H~~~eH~~---e~~~~vCPvC~~~v~ 84 (210)
+...+..||.|.+.+... .=|.|.=-..|. -.....||+|...+.
T Consensus 170 ~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 170 NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 344568999998865421 225553222222 124568999987654
No 121
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=40.33 E-value=27 Score=33.49 Aligned_cols=48 Identities=27% Similarity=0.597 Sum_probs=34.6
Q ss_pred cccCCCCCcch-hHHHhHhhhhhccCCCcccccCcccccchh--hhHHhhHh
Q 028361 44 CFPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAANLG--KDAAEHFM 92 (210)
Q Consensus 44 ~f~CP~C~e~~-d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~--~d~i~Hi~ 92 (210)
-|+||.|+-.. -.++|..|+.-.|.- .|.-.|--|+.+-- -|+..|++
T Consensus 263 ~ykCplCdmtc~~~ssL~~H~r~rHs~-dkpfKCd~Cd~~c~~esdL~kH~~ 313 (467)
T KOG3608|consen 263 CYKCPLCDMTCSSASSLTTHIRYRHSK-DKPFKCDECDTRCVRESDLAKHVQ 313 (467)
T ss_pred cccccccccCCCChHHHHHHHHhhhcc-CCCccccchhhhhccHHHHHHHHH
Confidence 57888887633 356788888888876 77788888887632 26777776
No 122
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=39.92 E-value=12 Score=25.68 Aligned_cols=34 Identities=32% Similarity=0.768 Sum_probs=13.0
Q ss_pred ccccccCCCCCcchhHHHhHhhhhhccCCCcccccCccccc
Q 028361 41 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
-..-+||| |+..|= --|-| +-.+..+++||-|..
T Consensus 12 d~~~~PC~-Cgf~IC--~~C~~----~i~~~~~g~CPgCr~ 45 (48)
T PF14570_consen 12 DKDFYPCE-CGFQIC--RFCYH----DILENEGGRCPGCRE 45 (48)
T ss_dssp CTT--SST-TS------HHHHH----HHTTSS-SB-TTT--
T ss_pred CCccccCc-CCCcHH--HHHHH----HHHhccCCCCCCCCC
Confidence 34568887 765432 22222 111245899999965
No 123
>PF14279 HNH_5: HNH endonuclease
Probab=39.82 E-value=14 Score=26.85 Aligned_cols=41 Identities=27% Similarity=0.637 Sum_probs=27.2
Q ss_pred CCCCCcchhHHHhHhhhhhccCC--------CcccccCcccccchhhhHHhhHh
Q 028361 47 CPFCYLEIEAHMICSHLQEEHCF--------EMKNAVCPLCAANLGKDAAEHFM 92 (210)
Q Consensus 47 CP~C~e~~d~~~L~~H~~~eH~~--------e~~~~vCPvC~~~v~~d~i~Hi~ 92 (210)
|.||.++++....- +||=. ..++ ||-.|...+|...-+++.
T Consensus 1 Ci~C~~~~~~~~~s----~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~vD~~l~ 49 (71)
T PF14279_consen 1 CIYCNKEKSESNFS----EEHIIPESLGGKLKINN-VCDKCNNKFGSKVDAELA 49 (71)
T ss_pred CccCCCCCCccCCC----ccccCchhcCCcccccc-hhHHHhHHHhHHHHHHHH
Confidence 89999877665422 34432 3455 999999998875544444
No 124
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=39.71 E-value=15 Score=30.94 Aligned_cols=33 Identities=30% Similarity=0.546 Sum_probs=19.6
Q ss_pred cCCCCCcchhHHHhHhhhhhccCCCccccc-----Ccccccchh
Q 028361 46 PCPFCYLEIEAHMICSHLQEEHCFEMKNAV-----CPLCAANLG 84 (210)
Q Consensus 46 ~CP~C~e~~d~~~L~~H~~~eH~~e~~~~v-----CPvC~~~v~ 84 (210)
.||||+.+-..+ .|.-+.+-.++| ||-|..+-+
T Consensus 2 ~CPfC~~~~tkV------iDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKV------IDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCee------eecccccccchhhhhhcccccccccc
Confidence 699997633222 233344444444 999988754
No 125
>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=39.56 E-value=6.4 Score=30.25 Aligned_cols=39 Identities=23% Similarity=0.515 Sum_probs=12.1
Q ss_pred ccCCCCCcchhHHHhH-hhhhhccCC-----------CcccccCcccccch
Q 028361 45 FPCPFCYLEIEAHMIC-SHLQEEHCF-----------EMKNAVCPLCAANL 83 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~-~H~~~eH~~-----------e~~~~vCPvC~~~v 83 (210)
=.||+|++.+....+. .=|..-|.+ +++.-+|++|..+.
T Consensus 15 E~C~~C~~~i~~~~~~~~~C~~GH~w~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 15 EKCPICGAPIPFDDLDEAQCENGHVWPRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp --------------SSEEE-TTS-EEEB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred ccccccccccccCCcCEeECCCCCEEeeeeeeeeeeccCCeeEcCCCCCEE
Confidence 3699999977655542 335677766 55667899998774
No 126
>PF15616 TerY-C: TerY-C metal binding domain
Probab=38.99 E-value=10 Score=31.03 Aligned_cols=45 Identities=20% Similarity=0.462 Sum_probs=29.7
Q ss_pred cccccCCCCCcchhHHHhHhhhhhccCCCc-ccccCcccccchhhhHH
Q 028361 42 KACFPCPFCYLEIEAHMICSHLQEEHCFEM-KNAVCPLCAANLGKDAA 88 (210)
Q Consensus 42 ~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~-~~~vCPvC~~~v~~d~i 88 (210)
.-.=.||+|+..+-++ +| =|-.-|+++. ..++||-|-..+.-..+
T Consensus 75 ~g~PgCP~CGn~~~fa-~C-~CGkl~Ci~g~~~~~CPwCg~~g~~~~~ 120 (131)
T PF15616_consen 75 IGAPGCPHCGNQYAFA-VC-GCGKLFCIDGEGEVTCPWCGNEGSFGAG 120 (131)
T ss_pred cCCCCCCCCcChhcEE-Ee-cCCCEEEeCCCCCEECCCCCCeeeeccc
Confidence 3446899999754432 23 4666688644 56899999987654433
No 127
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=38.91 E-value=5.8 Score=23.90 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=7.6
Q ss_pred ccccCcccccc
Q 028361 72 KNAVCPLCAAN 82 (210)
Q Consensus 72 ~~~vCPvC~~~ 82 (210)
.+..||+|...
T Consensus 34 ~~~~Cp~C~~~ 44 (45)
T cd00162 34 GKNTCPLCRTP 44 (45)
T ss_pred CcCCCCCCCCc
Confidence 35679988654
No 128
>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=38.46 E-value=12 Score=25.94 Aligned_cols=44 Identities=23% Similarity=0.431 Sum_probs=25.8
Q ss_pred cCccccCc-cccccccCCCCCcc--hhHHHhHhhhhhccCCCcccccCcccccchh
Q 028361 32 VDETEIDD-DVKACFPCPFCYLE--IEAHMICSHLQEEHCFEMKNAVCPLCAANLG 84 (210)
Q Consensus 32 ~~~~~~d~-d~~~~f~CP~C~e~--~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~ 84 (210)
++|++.++ +.-..++|+ ||-. +....|-.+ .--+-|+-|.-.|.
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 45554333 234789996 9874 444444443 33467999987653
No 129
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.94 E-value=20 Score=36.59 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=25.2
Q ss_pred ccccccCCCCCc-chhHHHhHhhhhhccCC
Q 028361 41 VKACFPCPFCYL-EIEAHMICSHLQEEHCF 69 (210)
Q Consensus 41 ~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~ 69 (210)
.+----|+||.+ -||...|..|+..+|.+
T Consensus 179 ~rGhp~C~~C~~~fld~~el~rH~~~~h~~ 208 (669)
T KOG2231|consen 179 CRGHPLCKFCHERFLDDDELYRHLRFDHEF 208 (669)
T ss_pred ccCCccchhhhhhhccHHHHHHhhccceeh
Confidence 344678999988 99999999999998887
No 130
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=37.88 E-value=17 Score=25.64 Aligned_cols=12 Identities=33% Similarity=0.844 Sum_probs=9.8
Q ss_pred ccccccCCCCCc
Q 028361 41 VKACFPCPFCYL 52 (210)
Q Consensus 41 ~~~~f~CP~C~e 52 (210)
.+..|.||.||.
T Consensus 11 ~~v~~~Cp~cGi 22 (55)
T PF13824_consen 11 AHVNFECPDCGI 22 (55)
T ss_pred cccCCcCCCCCC
Confidence 467899999975
No 131
>TIGR00165 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.
Probab=37.69 E-value=21 Score=26.19 Aligned_cols=30 Identities=17% Similarity=0.357 Sum_probs=19.8
Q ss_pred cccccCcccccchh------hhHHhhHhhhhcchhh
Q 028361 71 MKNAVCPLCAANLG------KDAAEHFMVQHASSLK 100 (210)
Q Consensus 71 ~~~~vCPvC~~~v~------~d~i~Hi~~qh~~~~K 100 (210)
.+.-+||+|...+. .+++..+..++|.++-
T Consensus 3 ~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~GkIlp 38 (70)
T TIGR00165 3 RRKKYCRFTAEGIQFIDYKDLDLLKKFISERGKILP 38 (70)
T ss_pred CCCCCCCccCCCCCcCCccCHHHHHHhcCCCCeEcC
Confidence 34567888876543 2677777777777763
No 132
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=36.86 E-value=20 Score=24.14 Aligned_cols=38 Identities=26% Similarity=0.487 Sum_probs=22.8
Q ss_pred ccccCccccccccCCCCCcchhHHHhHhhhhhccCCCcccccCccc
Q 028361 34 ETEIDDDVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLC 79 (210)
Q Consensus 34 ~~~~d~d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC 79 (210)
++-..-.....+.||.|+..+....=-. . .+...||.|
T Consensus 18 ~v~~~s~~~v~W~C~~Cgh~w~~~v~~R-------~-~~~~~CP~C 55 (55)
T PF14311_consen 18 EVTPGSNKKVWWKCPKCGHEWKASVNDR-------T-RRGKGCPYC 55 (55)
T ss_pred HhCcCCCCEEEEECCCCCCeeEccHhhh-------c-cCCCCCCCC
Confidence 3333334567799999987665432111 1 456789988
No 133
>PRK04023 DNA polymerase II large subunit; Validated
Probab=36.77 E-value=17 Score=38.73 Aligned_cols=39 Identities=23% Similarity=0.495 Sum_probs=22.8
Q ss_pred ccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 43 ACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
..|.||.|+..=...--|..|- .......||-|...+..
T Consensus 637 ~~frCP~CG~~Te~i~fCP~CG----~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRCG----IEVEEDECEKCGREPTP 675 (1121)
T ss_pred CcccCCCCCCCCCcceeCcccc----CcCCCCcCCCCCCCCCc
Confidence 4567777776545555566652 22333568888776543
No 134
>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=36.71 E-value=15 Score=25.42 Aligned_cols=10 Identities=30% Similarity=1.049 Sum_probs=8.5
Q ss_pred ccccCCCCCc
Q 028361 43 ACFPCPFCYL 52 (210)
Q Consensus 43 ~~f~CP~C~e 52 (210)
-.|.||+|+.
T Consensus 43 i~y~C~~Cg~ 52 (54)
T PF10058_consen 43 IQYRCPYCGA 52 (54)
T ss_pred eEEEcCCCCC
Confidence 3899999985
No 135
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=36.40 E-value=20 Score=33.71 Aligned_cols=40 Identities=23% Similarity=0.462 Sum_probs=29.4
Q ss_pred cccccCCCCCcchh--HHHhHhhhhhc-cCC-----CcccccCccccc
Q 028361 42 KACFPCPFCYLEIE--AHMICSHLQEE-HCF-----EMKNAVCPLCAA 81 (210)
Q Consensus 42 ~~~f~CP~C~e~~d--~~~L~~H~~~e-H~~-----e~~~~vCPvC~~ 81 (210)
...-.||.||...| +.+||.=|.-+ |+. +.+..+|+.|-+
T Consensus 4 ~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 4 ASTILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred CcccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCC
Confidence 35678999999888 88888766554 544 334478999974
No 136
>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=35.73 E-value=11 Score=28.64 Aligned_cols=8 Identities=50% Similarity=1.364 Sum_probs=6.6
Q ss_pred ccCCCCCc
Q 028361 45 FPCPFCYL 52 (210)
Q Consensus 45 f~CP~C~e 52 (210)
++||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T PF04267_consen 2 IPCPHCGP 9 (84)
T ss_dssp EEETTTEE
T ss_pred ccCCCCCc
Confidence 57999987
No 137
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.64 E-value=11 Score=34.76 Aligned_cols=41 Identities=29% Similarity=0.646 Sum_probs=25.6
Q ss_pred ccccCCCCCc--chhHHHh-HhhhhhccCCCccc-----ccCcccccch
Q 028361 43 ACFPCPFCYL--EIEAHMI-CSHLQEEHCFEMKN-----AVCPLCAANL 83 (210)
Q Consensus 43 ~~f~CP~C~e--~~d~~~L-~~H~~~eH~~e~~~-----~vCPvC~~~v 83 (210)
....||+|++ -+--... |.|+-=.-|.-+.- ..||-|.+.+
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred CCceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 4678999999 4555666 77753322322222 4799998764
No 138
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=35.40 E-value=27 Score=31.20 Aligned_cols=38 Identities=21% Similarity=0.399 Sum_probs=21.8
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchh
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLG 84 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~ 84 (210)
-.+...-||-|.-.= +| -|.-+ -+. ..-|||-|..+.+
T Consensus 188 ~~~~alIC~~C~hhn---gl-~~~~e-k~~--~efiC~~Cn~~n~ 225 (251)
T COG5415 188 SPFKALICPQCHHHN---GL-YRLAE-KPI--IEFICPHCNHKND 225 (251)
T ss_pred Cchhhhccccccccc---cc-ccccc-ccc--hheecccchhhcC
Confidence 456788899995411 11 11111 122 2469999998765
No 139
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=34.70 E-value=8.8 Score=30.62 Aligned_cols=13 Identities=31% Similarity=0.710 Sum_probs=10.1
Q ss_pred CCCCCcchhHHHh
Q 028361 47 CPFCYLEIEAHMI 59 (210)
Q Consensus 47 CP~C~e~~d~~~L 59 (210)
||.|+.++-|..|
T Consensus 1 CPvCg~~l~vt~l 13 (113)
T PF09862_consen 1 CPVCGGELVVTRL 13 (113)
T ss_pred CCCCCCceEEEEE
Confidence 9999888776655
No 140
>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=34.48 E-value=13 Score=27.95 Aligned_cols=18 Identities=28% Similarity=0.493 Sum_probs=10.7
Q ss_pred ccccccccCCCCCcchhH
Q 028361 39 DDVKACFPCPFCYLEIEA 56 (210)
Q Consensus 39 ~d~~~~f~CP~C~e~~d~ 56 (210)
-|+-+.|.||-|++.+++
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 467899999999986553
No 141
>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=33.55 E-value=19 Score=27.35 Aligned_cols=8 Identities=50% Similarity=1.580 Sum_probs=6.4
Q ss_pred ccCCCCCc
Q 028361 45 FPCPFCYL 52 (210)
Q Consensus 45 f~CP~C~e 52 (210)
++||+|+.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 57999984
No 142
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=32.95 E-value=18 Score=28.68 Aligned_cols=33 Identities=27% Similarity=0.628 Sum_probs=19.1
Q ss_pred ccccccCCCCCcchhHHHhHhhhhhccCCCccc----ccCcccccc
Q 028361 41 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKN----AVCPLCAAN 82 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~----~vCPvC~~~ 82 (210)
+...|.||||.-+= - -.|..+.+. .-|-||..-
T Consensus 20 ldt~FnClfcnHek----~-----v~~~~Dk~~~iG~~sC~iC~es 56 (109)
T KOG3214|consen 20 LDTQFNCLFCNHEK----S-----VSCTLDKKHNIGKASCRICEES 56 (109)
T ss_pred hheeeccCcccccc----c-----eeeeehhhcCcceeeeeehhhh
Confidence 44679999996532 1 123333333 448888654
No 143
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=32.72 E-value=20 Score=32.73 Aligned_cols=30 Identities=23% Similarity=0.637 Sum_probs=14.3
Q ss_pred CCCCCcchhHHH-hHhhhhhccCCCcccccCcccccc
Q 028361 47 CPFCYLEIEAHM-ICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 47 CP~C~e~~d~~~-L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
|=||+.+||-.- |..|.. +|.-.|-||.++
T Consensus 13 cwycnrefddekiliqhqk------akhfkchichkk 43 (341)
T KOG2893|consen 13 CWYCNREFDDEKILIQHQK------AKHFKCHICHKK 43 (341)
T ss_pred eeecccccchhhhhhhhhh------hccceeeeehhh
Confidence 555665554332 333332 233456666655
No 144
>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=32.61 E-value=9.3 Score=32.06 Aligned_cols=14 Identities=21% Similarity=0.477 Sum_probs=11.1
Q ss_pred cccccccCCCCCcc
Q 028361 40 DVKACFPCPFCYLE 53 (210)
Q Consensus 40 d~~~~f~CP~C~e~ 53 (210)
|....|.|||||-.
T Consensus 4 d~~~D~vcPwcylg 17 (209)
T cd03021 4 ELYYDVVSPYSYLA 17 (209)
T ss_pred EEEEeCCChHHHHH
Confidence 35678999999874
No 145
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=31.93 E-value=23 Score=28.24 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=17.4
Q ss_pred cccCcccccchh-----hhHHhhHhhhhcch
Q 028361 73 NAVCPLCAANLG-----KDAAEHFMVQHASS 98 (210)
Q Consensus 73 ~~vCPvC~~~v~-----~d~i~Hi~~qh~~~ 98 (210)
.|.||+|....+ ....-|++.-||-.
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~ 55 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGIS 55 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhccccc
Confidence 788999985433 24667777666654
No 146
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=31.85 E-value=21 Score=30.51 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=11.1
Q ss_pred ccCCCCCcchhHHH
Q 028361 45 FPCPFCYLEIEAHM 58 (210)
Q Consensus 45 f~CP~C~e~~d~~~ 58 (210)
=+||+|+.-+|-.+
T Consensus 155 P~CPlCg~PlDP~G 168 (171)
T PF11290_consen 155 PPCPLCGEPLDPEG 168 (171)
T ss_pred CCCCCCCCCCCCCC
Confidence 58999999887543
No 147
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=31.82 E-value=19 Score=30.41 Aligned_cols=41 Identities=29% Similarity=0.639 Sum_probs=26.4
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCC---Cc---ccccCcccccchh
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCF---EM---KNAVCPLCAANLG 84 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~---e~---~~~vCPvC~~~v~ 84 (210)
--.||.|+..++...-..|++-.|+. .+ +-..|+-|...+|
T Consensus 20 ~G~CaiC~~~l~~~~~~~~vDHDH~l~g~~TG~VRGLLC~~CN~~lG 66 (157)
T PHA02565 20 NGICPLCKRELDGDVSKNHLDHDHELNGPNAGRVRGLLCNLCNALEG 66 (157)
T ss_pred CCcCCCCCCccCCCccccccCCCCCCCCcccccccccCchhhhhhhh
Confidence 34799999877644333377767733 22 3356999987655
No 148
>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=31.53 E-value=13 Score=30.22 Aligned_cols=23 Identities=22% Similarity=0.592 Sum_probs=15.0
Q ss_pred ccccccCCCCCc-chhHHHhHhhh
Q 028361 41 VKACFPCPFCYL-EIEAHMICSHL 63 (210)
Q Consensus 41 ~~~~f~CP~C~e-~~d~~~L~~H~ 63 (210)
.-.+|.||||+. .--+..+....
T Consensus 3 ~~~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 3 IWSDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred EEecCcCccHHHHHHHHHHHHHhC
Confidence 456799999996 43444555443
No 149
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=31.52 E-value=12 Score=25.62 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=17.3
Q ss_pred cCCCCCcchhHHHhHhhhhhccCCCcccccCcccccch
Q 028361 46 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 46 ~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
+|+.|+..+-.-.- -.+.| - -||.-|..++
T Consensus 1 ~C~iCg~kigl~~~-~k~~D-----G--~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKR-FKIKD-----G--YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccc-eeccC-----c--cchHHHHHHh
Confidence 47888775544332 22222 2 3888888776
No 150
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=31.27 E-value=31 Score=31.51 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=21.5
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
-.+||.|++-+-...|-. +..|||-|...
T Consensus 27 ~~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEA----------NLNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHh----------cCCCCCCCCCC
Confidence 578999998666665543 23599999885
No 151
>PF14353 CpXC: CpXC protein
Probab=31.16 E-value=21 Score=27.87 Aligned_cols=16 Identities=25% Similarity=0.553 Sum_probs=12.2
Q ss_pred cccccCCCCCcchhHH
Q 028361 42 KACFPCPFCYLEIEAH 57 (210)
Q Consensus 42 ~~~f~CP~C~e~~d~~ 57 (210)
-..|.||.||..+-+.
T Consensus 36 l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCEEECCCCCCceecC
Confidence 3579999999866553
No 152
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.11 E-value=15 Score=23.48 Aligned_cols=27 Identities=33% Similarity=0.753 Sum_probs=15.3
Q ss_pred cCCCCCcchhHHHhHhhhhhccCCCcccccCccccc
Q 028361 46 PCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 46 ~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
.||-|...+....+ .+...-+||-|.-
T Consensus 1 ~CP~C~~~l~~~~~---------~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGTELEPVRL---------GDVEIDVCPSCGG 27 (41)
T ss_pred CcCCCCcccceEEE---------CCEEEEECCCCCe
Confidence 47888766665444 1223346777753
No 153
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=30.56 E-value=16 Score=25.71 Aligned_cols=43 Identities=28% Similarity=0.722 Sum_probs=32.6
Q ss_pred cccccCCCCCc--chhHHHhHhhhhhccCCCccc-ccCcccccchh
Q 028361 42 KACFPCPFCYL--EIEAHMICSHLQEEHCFEMKN-AVCPLCAANLG 84 (210)
Q Consensus 42 ~~~f~CP~C~e--~~d~~~L~~H~~~eH~~e~~~-~vCPvC~~~v~ 84 (210)
....+|=+|++ .--+..=|-|+.=.++++... .-||+|..++.
T Consensus 5 ~~~~~~~~~~~~~~~~~~~pCgH~I~~~~f~~~rYngCPfC~~~~~ 50 (55)
T PF14447_consen 5 QPEQPCVFCGFVGTKGTVLPCGHLICDNCFPGERYNGCPFCGTPFE 50 (55)
T ss_pred ccceeEEEccccccccccccccceeeccccChhhccCCCCCCCccc
Confidence 35677888876 456677788999889988754 67999988754
No 154
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=30.46 E-value=17 Score=28.54 Aligned_cols=31 Identities=19% Similarity=0.394 Sum_probs=20.8
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
..+..+.|+-|+..|..... .-..||.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQ------------RVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCCeeecCCc------------cCCcCcCcCCC
Confidence 46789999999875543211 11469999864
No 155
>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=30.40 E-value=14 Score=34.70 Aligned_cols=40 Identities=23% Similarity=0.434 Sum_probs=25.9
Q ss_pred cccCCCCCcchhHHHhHhhhhhcc-CCCcccccCcccccch
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEH-CFEMKNAVCPLCAANL 83 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH-~~e~~~~vCPvC~~~v 83 (210)
.-.||+|+.+---...|++|-... |.+..+.+|.+|...+
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 467999986555556777765433 4677889999998864
No 156
>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=30.28 E-value=8.7 Score=23.86 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=4.6
Q ss_pred cccccCccc
Q 028361 71 MKNAVCPLC 79 (210)
Q Consensus 71 ~~~~vCPvC 79 (210)
.....||+|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 334456665
No 157
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=30.22 E-value=20 Score=23.51 Aligned_cols=10 Identities=30% Similarity=0.866 Sum_probs=8.1
Q ss_pred cccCCCCCcc
Q 028361 44 CFPCPFCYLE 53 (210)
Q Consensus 44 ~f~CP~C~e~ 53 (210)
...||||+.-
T Consensus 29 ~~~CpYCg~~ 38 (40)
T PF10276_consen 29 PVVCPYCGTR 38 (40)
T ss_dssp EEEETTTTEE
T ss_pred eEECCCCCCE
Confidence 6899999863
No 158
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.11 E-value=22 Score=29.09 Aligned_cols=40 Identities=23% Similarity=0.688 Sum_probs=23.1
Q ss_pred ccccccCCCCCcchhHH-Hh-HhhhhhccCCCc---ccccCcccc
Q 028361 41 VKACFPCPFCYLEIEAH-MI-CSHLQEEHCFEM---KNAVCPLCA 80 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~-~L-~~H~~~eH~~e~---~~~vCPvC~ 80 (210)
....+.||.|.+.|... .| |-|---..+... ....||+|.
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 44678999998877666 22 222211111111 337899999
No 159
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.98 E-value=22 Score=37.24 Aligned_cols=44 Identities=27% Similarity=0.623 Sum_probs=36.6
Q ss_pred cCCCCCcchhHH---HhHhhhhhccCCCcccccCcccccc--hhhhHHh
Q 028361 46 PCPFCYLEIEAH---MICSHLQEEHCFEMKNAVCPLCAAN--LGKDAAE 89 (210)
Q Consensus 46 ~CP~C~e~~d~~---~L~~H~~~eH~~e~~~~vCPvC~~~--v~~d~i~ 89 (210)
+|--|...+|+. .+|-|.--.||++.+...||-|..- -++||++
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 899999988865 5899999999999999999999983 3345554
No 160
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=29.92 E-value=22 Score=29.60 Aligned_cols=33 Identities=24% Similarity=0.499 Sum_probs=18.4
Q ss_pred ccCCCCCcchhHHHhHhhhhhccCCCccc-----ccCcccccch
Q 028361 45 FPCPFCYLEIEAHMICSHLQEEHCFEMKN-----AVCPLCAANL 83 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~~~eH~~e~~~-----~vCPvC~~~v 83 (210)
..||||+.... |+-+.-.+...| --||-|...-
T Consensus 1 m~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCcc
Confidence 37999987431 222223333333 3499998763
No 161
>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=29.74 E-value=35 Score=31.06 Aligned_cols=29 Identities=24% Similarity=0.514 Sum_probs=21.4
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
-.+||-|++-+-...|-. +..|||-|...
T Consensus 26 ~~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELER----------NLEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHh----------hCCCCCCCCCc
Confidence 568999998766655544 23699999886
No 162
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=29.61 E-value=38 Score=30.03 Aligned_cols=52 Identities=23% Similarity=0.372 Sum_probs=33.7
Q ss_pred cccccccCCCCCcc-hhHHHhH--------hhhhhccCCCcccccCcccccchhhhHHhhHhhhhcc
Q 028361 40 DVKACFPCPFCYLE-IEAHMIC--------SHLQEEHCFEMKNAVCPLCAANLGKDAAEHFMVQHAS 97 (210)
Q Consensus 40 d~~~~f~CP~C~e~-~d~~~L~--------~H~~~eH~~e~~~~vCPvC~~~v~~d~i~Hi~~qh~~ 97 (210)
|+..++.||+|+-. --...+. -++ .-|||+.....||- |.|...++..+-|.
T Consensus 9 ~v~sD~vCPwC~ig~~rL~ka~~~~~~~~~v~i-~w~pf~l~p~~~~~-----g~~~~~~l~~k~g~ 69 (225)
T COG2761 9 DVFSDVVCPWCYIGKRRLEKALAEYPQEVRVEI-RWRPFELDPDLPPE-----GLDRKEYLAQKYGI 69 (225)
T ss_pred EEEeCCcCchhhcCHHHHHHHHHhcCcceeEEE-EecccccCCCCCcc-----cccHHHHHHHHhCc
Confidence 57788999999762 1111111 222 34889888888887 77888777744443
No 163
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=29.46 E-value=50 Score=30.42 Aligned_cols=29 Identities=24% Similarity=0.479 Sum_probs=21.8
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
-.+||-|++-+-...|-. +..|||-|...
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 468999998776666544 23699999885
No 164
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.11 E-value=23 Score=27.90 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=21.4
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccc
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
+.+..+.|+-|+..|.+... .-..||-|...
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 46788999999876655422 12359999864
No 165
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=29.03 E-value=24 Score=36.33 Aligned_cols=41 Identities=22% Similarity=0.407 Sum_probs=27.3
Q ss_pred cccccccCCCCCcch----hHHHhHhhhhhccCCCcccccCcccccc
Q 028361 40 DVKACFPCPFCYLEI----EAHMICSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 40 d~~~~f~CP~C~e~~----d~~~L~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
+....+.||.|+..+ +...|.||-=..| +..+-.||-|...
T Consensus 440 ~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 440 DCGYIAECPNCDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred cCCCcccCCCCCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 456679999998643 3345555522212 5677899999986
No 166
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.89 E-value=15 Score=35.05 Aligned_cols=47 Identities=23% Similarity=0.490 Sum_probs=27.8
Q ss_pred ccccccccCCCCCcchhHHH--hHhhhhhccCC---CcccccCcccccchhh
Q 028361 39 DDVKACFPCPFCYLEIEAHM--ICSHLQEEHCF---EMKNAVCPLCAANLGK 85 (210)
Q Consensus 39 ~d~~~~f~CP~C~e~~d~~~--L~~H~~~eH~~---e~~~~vCPvC~~~v~~ 85 (210)
++++..+.||.|.+.|.... =|-|.-=..|. -.....||+|...++.
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 35667899999988665442 34442211111 1223589999987654
No 167
>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=28.82 E-value=12 Score=30.01 Aligned_cols=15 Identities=33% Similarity=0.578 Sum_probs=11.2
Q ss_pred ccccccCCCCCcchh
Q 028361 41 VKACFPCPFCYLEIE 55 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d 55 (210)
...+|.||||+-...
T Consensus 3 ~~~D~~cP~cy~~~~ 17 (192)
T cd03022 3 FYFDFSSPYSYLAHE 17 (192)
T ss_pred EEEeCCChHHHHHHH
Confidence 456789999987433
No 168
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=28.66 E-value=29 Score=31.47 Aligned_cols=41 Identities=17% Similarity=0.425 Sum_probs=28.9
Q ss_pred ccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhhhHHhhH
Q 028361 41 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKDAAEHF 91 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d~i~Hi 91 (210)
......||.|+.. ++ +.| ++....||.-|..=|.+++|.+-
T Consensus 8 ~~~~~~Cp~Cg~~-~i------v~d---~~~Ge~vC~~CG~Vl~e~~iD~g 48 (310)
T PRK00423 8 EEEKLVCPECGSD-KL------IYD---YERGEIVCADCGLVIEENIIDQG 48 (310)
T ss_pred cccCCcCcCCCCC-Ce------eEE---CCCCeEeecccCCcccccccccC
Confidence 3344679999862 11 112 35778999999999999988665
No 169
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.61 E-value=28 Score=23.96 Aligned_cols=12 Identities=25% Similarity=0.703 Sum_probs=9.5
Q ss_pred ccccccCCCCCc
Q 028361 41 VKACFPCPFCYL 52 (210)
Q Consensus 41 ~~~~f~CP~C~e 52 (210)
......||||+.
T Consensus 21 ~~~~irCp~Cg~ 32 (49)
T COG1996 21 ETRGIRCPYCGS 32 (49)
T ss_pred ccCceeCCCCCc
Confidence 456789999985
No 170
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=27.85 E-value=20 Score=30.93 Aligned_cols=19 Identities=26% Similarity=0.384 Sum_probs=0.0
Q ss_pred ccCCCCCcchhHHHhHhhh
Q 028361 45 FPCPFCYLEIEAHMICSHL 63 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~ 63 (210)
..||.||+-+-+..+-.|+
T Consensus 169 ~~cPitGe~IP~~e~~eHm 187 (229)
T PF12230_consen 169 IICPITGEMIPADEMDEHM 187 (229)
T ss_dssp -------------------
T ss_pred ccccccccccccccccccc
Confidence 4555555555555555553
No 171
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=27.81 E-value=25 Score=25.36 Aligned_cols=11 Identities=36% Similarity=0.751 Sum_probs=8.0
Q ss_pred cccccCCCCCc
Q 028361 42 KACFPCPFCYL 52 (210)
Q Consensus 42 ~~~f~CP~C~e 52 (210)
...+.|-+|++
T Consensus 3 k~~~~C~~Cg~ 13 (69)
T PF09706_consen 3 KKKYNCIFCGE 13 (69)
T ss_pred CCCCcCcCCCC
Confidence 34678889984
No 172
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=27.64 E-value=36 Score=21.24 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=9.4
Q ss_pred ccccccccCCCCCc
Q 028361 39 DDVKACFPCPFCYL 52 (210)
Q Consensus 39 ~d~~~~f~CP~C~e 52 (210)
.+......||+|+.
T Consensus 12 ~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 12 LKPGDPIRCPECGH 25 (32)
T ss_dssp BSTSSTSSBSSSS-
T ss_pred cCCCCcEECCcCCC
Confidence 34556689999985
No 173
>PRK12722 transcriptional activator FlhC; Provisional
Probab=27.26 E-value=47 Score=28.73 Aligned_cols=32 Identities=22% Similarity=0.434 Sum_probs=21.5
Q ss_pred cccccccCCCCCcchhHHHhHhhhhhccCCCc-ccccCccccc
Q 028361 40 DVKACFPCPFCYLEIEAHMICSHLQEEHCFEM-KNAVCPLCAA 81 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~-~~~vCPvC~~ 81 (210)
++-..-+|..|+-.|=+ |..|. .+.+||+|.-
T Consensus 130 ~~L~l~~C~~Cgg~fv~----------~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 130 GMLQLSSCNCCGGHFVT----------HAHDPVGSFVCGLCQP 162 (187)
T ss_pred CcEeeccCCCCCCCeec----------cccccCCCCcCCCCCC
Confidence 35677899999875521 22344 4579999975
No 174
>TIGR00618 sbcc exonuclease SbcC. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.12 E-value=20 Score=37.58 Aligned_cols=33 Identities=15% Similarity=0.112 Sum_probs=21.1
Q ss_pred ccccccCCCCCcchhHHHhHhhhhhccCC----C--cccccCcccccchhh
Q 028361 41 VKACFPCPFCYLEIEAHMICSHLQEEHCF----E--MKNAVCPLCAANLGK 85 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~~L~~H~~~eH~~----e--~~~~vCPvC~~~v~~ 85 (210)
....=|||+||. .+||+ . ...++||.|......
T Consensus 498 l~~~~~cplcgs------------~~hp~~~~~~~~~~~~~~~~~~~~~~~ 536 (1042)
T TIGR00618 498 ELQEEPCPLCGS------------CIHPNPARQDIDNPGPLTRRMQRGEQT 536 (1042)
T ss_pred cCCCCCCCCCCC------------CCCCChhhccCCCCCHHHHHHHHHHHH
Confidence 446679999987 22331 1 135789999886544
No 175
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=26.86 E-value=35 Score=24.42 Aligned_cols=46 Identities=15% Similarity=0.265 Sum_probs=20.4
Q ss_pred cccccccCC--CCCcchhHHHhHhhhhhccC----CCcccccCcccccchhh
Q 028361 40 DVKACFPCP--FCYLEIEAHMICSHLQEEHC----FEMKNAVCPLCAANLGK 85 (210)
Q Consensus 40 d~~~~f~CP--~C~e~~d~~~L~~H~~~eH~----~e~~~~vCPvC~~~v~~ 85 (210)
+..+...|| -|+.-|=..=|-..+..... +....|.||.|...|.-
T Consensus 16 ~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 16 GEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp -----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 344577886 88877777777777665333 44555779999987653
No 176
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.79 E-value=16 Score=28.09 Aligned_cols=17 Identities=35% Similarity=0.735 Sum_probs=12.9
Q ss_pred cCccccccccCCCCCcc
Q 028361 37 IDDDVKACFPCPFCYLE 53 (210)
Q Consensus 37 ~d~d~~~~f~CP~C~e~ 53 (210)
.+.-++..+.||+|+..
T Consensus 28 ie~~~~~~~~Cp~C~~~ 44 (89)
T COG1997 28 IEAQQRAKHVCPFCGRT 44 (89)
T ss_pred HHHHHhcCCcCCCCCCc
Confidence 34457889999999864
No 177
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.79 E-value=29 Score=27.68 Aligned_cols=16 Identities=25% Similarity=0.582 Sum_probs=12.7
Q ss_pred cccCCCCCcchhHHHh
Q 028361 44 CFPCPFCYLEIEAHMI 59 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L 59 (210)
...||-||+.|+-..+
T Consensus 49 ~t~CP~Cg~~~e~~fv 64 (115)
T COG1885 49 STSCPKCGEPFESAFV 64 (115)
T ss_pred cccCCCCCCccceeEE
Confidence 4689999999986544
No 178
>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=26.56 E-value=23 Score=33.72 Aligned_cols=35 Identities=17% Similarity=0.501 Sum_probs=22.3
Q ss_pred ccccCCCCCc--chhHHHh-HhhhhhccCCCcccccCcccccch
Q 028361 43 ACFPCPFCYL--EIEAHMI-CSHLQEEHCFEMKNAVCPLCAANL 83 (210)
Q Consensus 43 ~~f~CP~C~e--~~d~~~L-~~H~~~eH~~e~~~~vCPvC~~~v 83 (210)
.-..||||+. --+...| |.||. ..+..||-|....
T Consensus 9 C~~~C~wC~~p~~~~~~~~~c~~C~------~~~~~C~yC~~~~ 46 (404)
T TIGR03278 9 CRGFCRYCYFKKVDDEQPFGCKNCP------PGTKGCDYCTRSV 46 (404)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCcCC------CCCCCCCCCCchh
Confidence 3467999986 3344445 55552 2366899997764
No 179
>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=26.55 E-value=18 Score=24.76 Aligned_cols=10 Identities=50% Similarity=1.195 Sum_probs=8.2
Q ss_pred ccccCCCCCc
Q 028361 43 ACFPCPFCYL 52 (210)
Q Consensus 43 ~~f~CP~C~e 52 (210)
..+.||+|+.
T Consensus 5 ~d~~Cp~C~~ 14 (98)
T cd02972 5 FDPLCPYCYL 14 (98)
T ss_pred ECCCCHhHHh
Confidence 4678999987
No 180
>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=26.19 E-value=40 Score=23.72 Aligned_cols=19 Identities=16% Similarity=0.513 Sum_probs=13.1
Q ss_pred ccccCCCCCcchhHHHhHh
Q 028361 43 ACFPCPFCYLEIEAHMICS 61 (210)
Q Consensus 43 ~~f~CP~C~e~~d~~~L~~ 61 (210)
....||+|.-.+|-..|..
T Consensus 6 niL~Cp~ck~pL~~~~l~~ 24 (68)
T PF03966_consen 6 NILACPVCKGPLDWEALVE 24 (68)
T ss_dssp GTBB-TTTSSBEHHHHHHH
T ss_pred hhhcCCCCCCcchHHHHHH
Confidence 3568999987887666665
No 181
>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=26.04 E-value=24 Score=27.79 Aligned_cols=18 Identities=28% Similarity=0.586 Sum_probs=11.7
Q ss_pred ccccCCCCCc-chhHHHhH
Q 028361 43 ACFPCPFCYL-EIEAHMIC 60 (210)
Q Consensus 43 ~~f~CP~C~e-~~d~~~L~ 60 (210)
..|.||||.. +=.+..+.
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~ 41 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWV 41 (178)
T ss_pred ECCCCcchhhhhHHHHHHH
Confidence 4799999976 43343343
No 182
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=26.04 E-value=21 Score=27.45 Aligned_cols=13 Identities=31% Similarity=0.746 Sum_probs=11.2
Q ss_pred cccccccCCCCCc
Q 028361 40 DVKACFPCPFCYL 52 (210)
Q Consensus 40 d~~~~f~CP~C~e 52 (210)
-+.+.|.|+||+.
T Consensus 32 ~Qhaky~CsfCGK 44 (92)
T KOG0402|consen 32 QQHAKYTCSFCGK 44 (92)
T ss_pred HHhhhhhhhhcch
Confidence 4678999999997
No 183
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.85 E-value=29 Score=35.17 Aligned_cols=39 Identities=15% Similarity=0.377 Sum_probs=25.9
Q ss_pred cccccccCCCCCcchhH----HHh-HhhhhhccCCCcccccCcccccc
Q 028361 40 DVKACFPCPFCYLEIEA----HMI-CSHLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 40 d~~~~f~CP~C~e~~d~----~~L-~~H~~~eH~~e~~~~vCPvC~~~ 82 (210)
+....+.||.|+-.+.. ..| |.||.-. ...-.||-|...
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 35667999999874443 235 6666531 236799999875
No 184
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=25.55 E-value=49 Score=28.27 Aligned_cols=35 Identities=20% Similarity=0.530 Sum_probs=23.1
Q ss_pred ccccccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 41 VKACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
....|.||-|..-+....-+.+ .-.||.|.+.+-.
T Consensus 110 ~~~~y~C~~~~~r~sfdeA~~~----------~F~Cp~Cg~~L~~ 144 (176)
T COG1675 110 ENNYYVCPNCHVKYSFDEAMEL----------GFTCPKCGEDLEE 144 (176)
T ss_pred cCCceeCCCCCCcccHHHHHHh----------CCCCCCCCchhhh
Confidence 4567999999764433333332 1599999988644
No 185
>PF14968 CCDC84: Coiled coil protein 84
Probab=25.51 E-value=35 Score=32.00 Aligned_cols=20 Identities=35% Similarity=0.732 Sum_probs=15.6
Q ss_pred CccccccccCCCCCcchhHH
Q 028361 38 DDDVKACFPCPFCYLEIEAH 57 (210)
Q Consensus 38 d~d~~~~f~CP~C~e~~d~~ 57 (210)
+.+.+..|=|+||+.++...
T Consensus 52 ~~~~~~~fWC~fC~~ev~~~ 71 (336)
T PF14968_consen 52 DPEHRNRFWCVFCDCEVREH 71 (336)
T ss_pred CccccceeEeeCccchhhhc
Confidence 34577889999999888755
No 186
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.08 E-value=39 Score=22.10 Aligned_cols=11 Identities=36% Similarity=0.809 Sum_probs=8.2
Q ss_pred cccccCCCCCc
Q 028361 42 KACFPCPFCYL 52 (210)
Q Consensus 42 ~~~f~CP~C~e 52 (210)
+..|.||+|+.
T Consensus 16 ~~g~~CP~Cg~ 26 (46)
T PF12760_consen 16 PDGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCCC
Confidence 34588999985
No 187
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.01 E-value=34 Score=24.14 Aligned_cols=10 Identities=50% Similarity=1.088 Sum_probs=8.5
Q ss_pred cccCCCCCcc
Q 028361 44 CFPCPFCYLE 53 (210)
Q Consensus 44 ~f~CP~C~e~ 53 (210)
..+||||+..
T Consensus 35 ~~pC~fCg~~ 44 (57)
T PF06221_consen 35 LGPCPFCGTP 44 (57)
T ss_pred cCcCCCCCCc
Confidence 6899999974
No 188
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=24.87 E-value=32 Score=29.46 Aligned_cols=26 Identities=27% Similarity=0.548 Sum_probs=16.1
Q ss_pred cccCCCCCcchhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
.-.||-||-.-- ..+.|+-|..+|-.
T Consensus 93 l~~CP~CGh~k~----------------a~~LC~~Cy~kV~k 118 (176)
T KOG4080|consen 93 LNTCPACGHIKP----------------AHTLCDYCYAKVHK 118 (176)
T ss_pred cccCcccCcccc----------------ccccHHHHHHHHHH
Confidence 457999974332 24567777776543
No 189
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.86 E-value=40 Score=31.69 Aligned_cols=23 Identities=35% Similarity=0.912 Sum_probs=19.1
Q ss_pred cccCCCCCcchhHHHhHhhhhhcc
Q 028361 44 CFPCPFCYLEIEAHMICSHLQEEH 67 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~eH 67 (210)
+.-||||.--+.....|.|++ .|
T Consensus 2 e~iCP~CkLsv~~~~m~~Hie-aH 24 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIE-AH 24 (393)
T ss_pred cccccceecccCHHHHHHHHH-hh
Confidence 457999988888889999998 34
No 190
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=24.66 E-value=35 Score=35.60 Aligned_cols=68 Identities=18% Similarity=0.308 Sum_probs=51.3
Q ss_pred cccCCCCCcch-hHHHhHhhhhhccCCCcccccCcccccch--hhhHHhhHhhhhcchh----hhhhccccCCCCCC
Q 028361 44 CFPCPFCYLEI-EAHMICSHLQEEHCFEMKNAVCPLCAANL--GKDAAEHFMVQHASSL----KRRRKCLKSGLRNG 113 (210)
Q Consensus 44 ~f~CP~C~e~~-d~~~L~~H~~~eH~~e~~~~vCPvC~~~v--~~d~i~Hi~~qh~~~~----Krr~r~rk~~~~s~ 113 (210)
-|.|-.|++-| ..++|..|.-+ |.- -+.--|-||-+-. .-.++.|.+|.-|--. |=.+|+.-+|+||+
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYE-HsG-qRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQ 968 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYE-HSG-QRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQ 968 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhh-hcC-CCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHh
Confidence 49999999855 67889998744 665 4667899997753 4488999998777632 55667888888885
No 191
>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=24.62 E-value=50 Score=19.53 Aligned_cols=19 Identities=26% Similarity=0.651 Sum_probs=9.6
Q ss_pred ccCCCCCcchh-HHHhHhhh
Q 028361 45 FPCPFCYLEIE-AHMICSHL 63 (210)
Q Consensus 45 f~CP~C~e~~d-~~~L~~H~ 63 (210)
|-|.+|...|. ...+..|+
T Consensus 4 ~~C~~C~~~~~~~~~~~~H~ 23 (35)
T smart00451 4 FYCKLCNVTFTDEISVEAHL 23 (35)
T ss_pred eEccccCCccCCHHHHHHHH
Confidence 44666655443 44444444
No 192
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=24.41 E-value=47 Score=19.00 Aligned_cols=19 Identities=21% Similarity=0.420 Sum_probs=10.4
Q ss_pred ccCCCCCcc-hhHHHhHhhh
Q 028361 45 FPCPFCYLE-IEAHMICSHL 63 (210)
Q Consensus 45 f~CP~C~e~-~d~~~L~~H~ 63 (210)
|-|+.|+.. -+...+..|+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~ 21 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHM 21 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCT
T ss_pred CCcccCCCCcCCHHHHHHHH
Confidence 556667663 3445555554
No 193
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=24.24 E-value=23 Score=32.52 Aligned_cols=44 Identities=20% Similarity=0.541 Sum_probs=32.2
Q ss_pred ccccccCCCCCcchhHHHhHhh---hhhccCCCcccccCcccccchh
Q 028361 41 VKACFPCPFCYLEIEAHMICSH---LQEEHCFEMKNAVCPLCAANLG 84 (210)
Q Consensus 41 ~~~~f~CP~C~e~~d~~~L~~H---~~~eH~~e~~~~vCPvC~~~v~ 84 (210)
.-..+-||-|...+......|+ +.=.=+--.+...||.|+..+|
T Consensus 45 ~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPPIFQCDNGHLACSSCRTKVSNKCPTCRLPIG 91 (299)
T ss_pred chhhccCchhhccCcccceecCCCcEehhhhhhhhcccCCccccccc
Confidence 3456889999999998888874 3322333355678999999988
No 194
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.57 E-value=44 Score=35.25 Aligned_cols=35 Identities=20% Similarity=0.445 Sum_probs=24.2
Q ss_pred cccccCCCCCcchhHHHhHhhhhhccCCCcccccCccccc
Q 028361 42 KACFPCPFCYLEIEAHMICSHLQEEHCFEMKNAVCPLCAA 81 (210)
Q Consensus 42 ~~~f~CP~C~e~~d~~~L~~H~~~eH~~e~~~~vCPvC~~ 81 (210)
-..+.||.|+..|....-. ...|.+..+.||.|.-
T Consensus 248 s~~~~c~~~g~~~~~~~~~-----~FSfNsp~G~Cp~C~G 282 (924)
T TIGR00630 248 SKHAACPECGFSLPELEPR-----LFSFNSPYGACPECSG 282 (924)
T ss_pred hhcccCcccCcccCcCChh-----hcCCCCCcCCCCCCcc
Confidence 3569999999766532221 2467777899999954
No 195
>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=23.33 E-value=45 Score=29.01 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=7.9
Q ss_pred ccccCcccccc
Q 028361 72 KNAVCPLCAAN 82 (210)
Q Consensus 72 ~~~vCPvC~~~ 82 (210)
...+||.|.+.
T Consensus 34 ~v~~C~~Cg~~ 44 (236)
T PF04981_consen 34 EVTICPKCGRY 44 (236)
T ss_pred CceECCCCCCE
Confidence 45679999763
No 196
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=23.30 E-value=34 Score=22.38 Aligned_cols=8 Identities=50% Similarity=1.065 Sum_probs=3.8
Q ss_pred ccCCCCCc
Q 028361 45 FPCPFCYL 52 (210)
Q Consensus 45 f~CP~C~e 52 (210)
-|||.|+-
T Consensus 4 ~pCP~CGG 11 (40)
T PF08273_consen 4 GPCPICGG 11 (40)
T ss_dssp E--TTTT-
T ss_pred CCCCCCcC
Confidence 47999964
No 197
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=23.11 E-value=11 Score=25.49 Aligned_cols=8 Identities=38% Similarity=1.140 Sum_probs=3.0
Q ss_pred ccCccccc
Q 028361 74 AVCPLCAA 81 (210)
Q Consensus 74 ~vCPvC~~ 81 (210)
-.||||.+
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 45888864
No 198
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=23.10 E-value=38 Score=24.91 Aligned_cols=8 Identities=50% Similarity=1.451 Sum_probs=4.2
Q ss_pred ccCCCCCc
Q 028361 45 FPCPFCYL 52 (210)
Q Consensus 45 f~CP~C~e 52 (210)
+.||+|+.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 35555544
No 199
>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=23.09 E-value=16 Score=28.34 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=16.0
Q ss_pred ccccCCCCCc-chhHHHhHhhh
Q 028361 43 ACFPCPFCYL-EIEAHMICSHL 63 (210)
Q Consensus 43 ~~f~CP~C~e-~~d~~~L~~H~ 63 (210)
..|.||+|.. .-.+..|..+.
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 4799999987 66677888775
No 200
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.00 E-value=38 Score=37.10 Aligned_cols=21 Identities=24% Similarity=0.268 Sum_probs=12.8
Q ss_pred CChhHHHHHHhHhHHHHHHHh
Q 028361 186 GHEENIEEKMQRATFVQQLIM 206 (210)
Q Consensus 186 ls~~d~eEr~~R~eFVQgLll 206 (210)
++..--+==.+=+.||-.||-
T Consensus 839 l~~~aa~yl~~va~fiDdLL~ 859 (1337)
T PRK14714 839 LSDGAAEYLLKVAKFVDDLLE 859 (1337)
T ss_pred cchHHHHHHHHHHHHHHHHHH
Confidence 444444444567888888873
No 201
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=22.91 E-value=54 Score=35.69 Aligned_cols=47 Identities=26% Similarity=0.504 Sum_probs=31.2
Q ss_pred ccCccccCccccccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 31 IVDETEIDDDVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 31 ~~~~~~~d~d~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
+|-|++ -+++-|.||-|.. +|...+- ----||.-.-.||.|...+.+
T Consensus 673 gITeVd---PL~phy~c~~c~~~ef~~~~~-----~~sg~dlp~k~cp~c~~~~~~ 720 (1213)
T TIGR01405 673 GITEVN---PLPPHYLCPNCKYSEFITDGS-----VGSGFDLPDKDCPKCGAPLKK 720 (1213)
T ss_pred cCCCcC---CCcccccCccccccccccccc-----ccccccCccccCccccccccc
Confidence 344553 4889999999954 6654431 113466677789999987544
No 202
>PF14369 zf-RING_3: zinc-finger
Probab=22.52 E-value=41 Score=21.22 Aligned_cols=9 Identities=33% Similarity=0.788 Sum_probs=7.5
Q ss_pred cCCCCCcch
Q 028361 46 PCPFCYLEI 54 (210)
Q Consensus 46 ~CP~C~e~~ 54 (210)
.||.|+-+|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 799998765
No 203
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.35 E-value=38 Score=37.02 Aligned_cols=21 Identities=24% Similarity=0.350 Sum_probs=12.0
Q ss_pred cccCCCCCcchhHHHhHhhhhh
Q 028361 44 CFPCPFCYLEIEAHMICSHLQE 65 (210)
Q Consensus 44 ~f~CP~C~e~~d~~~L~~H~~~ 65 (210)
.+.||-|+...- ...|..|-.
T Consensus 667 ~rkCPkCG~~t~-~~fCP~CGs 687 (1337)
T PRK14714 667 RRRCPSCGTETY-ENRCPDCGT 687 (1337)
T ss_pred EEECCCCCCccc-cccCcccCC
Confidence 578888876321 236655543
No 204
>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=22.21 E-value=14 Score=29.55 Aligned_cols=19 Identities=32% Similarity=0.670 Sum_probs=12.1
Q ss_pred cccccCCCCCc-chhHHHhH
Q 028361 42 KACFPCPFCYL-EIEAHMIC 60 (210)
Q Consensus 42 ~~~f~CP~C~e-~~d~~~L~ 60 (210)
-..|.||||+- .--+..|.
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 45789999986 33333343
No 205
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.04 E-value=36 Score=33.06 Aligned_cols=37 Identities=16% Similarity=0.391 Sum_probs=21.3
Q ss_pred ccccCCCCCcchh----HHHhHh-hhhhccCCCcccccCcccccc
Q 028361 43 ACFPCPFCYLEIE----AHMICS-HLQEEHCFEMKNAVCPLCAAN 82 (210)
Q Consensus 43 ~~f~CP~C~e~~d----~~~L~~-H~~~eH~~e~~~~vCPvC~~~ 82 (210)
....||.|+-.+. ...|.| ||.-.. .-+-.||.|...
T Consensus 221 ~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~---~~~~~Cp~C~s~ 262 (505)
T TIGR00595 221 YILCCPNCDVSLTYHKKEGKLRCHYCGYQE---PIPKTCPQCGSE 262 (505)
T ss_pred CccCCCCCCCceEEecCCCeEEcCCCcCcC---CCCCCCCCCCCC
Confidence 3467999985443 234444 443221 224689999874
No 206
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=21.89 E-value=43 Score=27.45 Aligned_cols=34 Identities=18% Similarity=0.215 Sum_probs=24.1
Q ss_pred cccccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccchhhh
Q 028361 40 DVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGKD 86 (210)
Q Consensus 40 d~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~d 86 (210)
++-....||-|+. =||..- .++|||-|..-.-..
T Consensus 5 elGtKr~Cp~cg~kFYDLnk-------------~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDLNR-------------RPAVSPYTGEQFPPE 39 (129)
T ss_pred hhCccccCCCcCccccccCC-------------CCccCCCcCCccCcc
Confidence 4556788999987 666663 257999998765444
No 207
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=21.82 E-value=39 Score=28.22 Aligned_cols=32 Identities=22% Similarity=0.593 Sum_probs=19.3
Q ss_pred cCCCCCc-chhHHHhHhhhhhccCCCccccc-----Ccccccchh
Q 028361 46 PCPFCYL-EIEAHMICSHLQEEHCFEMKNAV-----CPLCAANLG 84 (210)
Q Consensus 46 ~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~v-----CPvC~~~v~ 84 (210)
.||||+. +--| .|.-+.+..+.| |+.|..+-+
T Consensus 2 ~CP~C~~~dtkV-------iDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRV-------LDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEe-------eeccccCCCCeeeecccCCccCCccc
Confidence 6999986 3322 233344444444 999998744
No 208
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=21.81 E-value=39 Score=33.01 Aligned_cols=21 Identities=29% Similarity=0.578 Sum_probs=15.6
Q ss_pred hccCCCcccccCcccccchhh
Q 028361 65 EEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 65 ~eH~~e~~~~vCPvC~~~v~~ 85 (210)
.+.-.+++..|||||...+|.
T Consensus 29 ~~~~~~PNt~vcpv~lg~PG~ 49 (474)
T PRK05477 29 TDFGAEPNTNVCPVCLGLPGA 49 (474)
T ss_pred cccCCCCCCCcCccccCCCCC
Confidence 333446788999999998765
No 209
>PF14828 Amnionless: Amnionless
Probab=21.70 E-value=44 Score=32.20 Aligned_cols=41 Identities=29% Similarity=0.686 Sum_probs=26.9
Q ss_pred ccCCCCCcchhHHHhHhhh----hhccCCCc---ccccCcccccchhhh
Q 028361 45 FPCPFCYLEIEAHMICSHL----QEEHCFEM---KNAVCPLCAANLGKD 86 (210)
Q Consensus 45 f~CP~C~e~~d~~~L~~H~----~~eH~~e~---~~~vCPvC~~~v~~d 86 (210)
-.|+ |+.+.-...+|..+ ..-||.++ .-.-||||-++|...
T Consensus 192 ~gC~-C~n~~~l~~ICs~v~~~C~~~~C~~pl~P~GhCC~iCGa~v~~~ 239 (437)
T PF14828_consen 192 SGCP-CGNDEVLEWICSNVLQRCPKPHCRSPLRPEGHCCPICGAIVTLE 239 (437)
T ss_pred ccCc-cCcccchhhhhHHhhCcCCCCccCCCCCCCCCchhhcceEEEEe
Confidence 4566 77777777777654 44555544 335599999987543
No 210
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=21.52 E-value=22 Score=33.37 Aligned_cols=19 Identities=37% Similarity=0.721 Sum_probs=15.1
Q ss_pred cCCCcccccCcccccchhh
Q 028361 67 HCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 67 H~~e~~~~vCPvC~~~v~~ 85 (210)
|.-+.-.+|||||..+++.
T Consensus 169 h~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 169 HMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred HhhhhHhhhhhHhhhhccc
Confidence 6667778899999998653
No 211
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=21.14 E-value=43 Score=21.38 Aligned_cols=9 Identities=33% Similarity=0.718 Sum_probs=6.2
Q ss_pred cccCCCCCc
Q 028361 44 CFPCPFCYL 52 (210)
Q Consensus 44 ~f~CP~C~e 52 (210)
+..||+|..
T Consensus 5 ~v~CP~C~s 13 (36)
T PF03811_consen 5 DVHCPRCQS 13 (36)
T ss_pred eeeCCCCCC
Confidence 467888865
No 212
>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=20.52 E-value=51 Score=32.27 Aligned_cols=27 Identities=26% Similarity=0.666 Sum_probs=21.9
Q ss_pred ccCcccccch--hhhHHhhHhhhhcchhh
Q 028361 74 AVCPLCAANL--GKDAAEHFMVQHASSLK 100 (210)
Q Consensus 74 ~vCPvC~~~v--~~d~i~Hi~~qh~~~~K 100 (210)
-+||+|..+- ..++..|+-.+|-.-++
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 4699999874 34899999999988664
No 213
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=20.48 E-value=45 Score=22.65 Aligned_cols=9 Identities=44% Similarity=1.139 Sum_probs=5.5
Q ss_pred cccCCCCCc
Q 028361 44 CFPCPFCYL 52 (210)
Q Consensus 44 ~f~CP~C~e 52 (210)
-++||.||-
T Consensus 9 G~~CPgCG~ 17 (52)
T PF10825_consen 9 GIPCPGCGM 17 (52)
T ss_pred CCCCCCCcH
Confidence 356777764
No 214
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=20.36 E-value=65 Score=24.10 Aligned_cols=29 Identities=21% Similarity=0.554 Sum_probs=17.7
Q ss_pred cccccCcccccchh------hhHHhhHhhhhcchh
Q 028361 71 MKNAVCPLCAANLG------KDAAEHFMVQHASSL 99 (210)
Q Consensus 71 ~~~~vCPvC~~~v~------~d~i~Hi~~qh~~~~ 99 (210)
.+.-+||+|...+. .+++.++...+|.++
T Consensus 12 ~r~k~c~~c~~~~~~iDYKnv~lL~~Fis~~GkIl 46 (79)
T PRK00391 12 RRKKVCRFCAEKIEYIDYKDVELLKKFISERGKIL 46 (79)
T ss_pred CCCCCCcccCCCCCcCCccCHHHHHHhcCCCceEc
Confidence 34456777776652 256666666666665
No 215
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=20.25 E-value=65 Score=35.71 Aligned_cols=47 Identities=23% Similarity=0.498 Sum_probs=30.6
Q ss_pred ccCccccCccccccccCCCCCc-chhHHHhHhhhhhccCCCcccccCcccccchhh
Q 028361 31 IVDETEIDDDVKACFPCPFCYL-EIEAHMICSHLQEEHCFEMKNAVCPLCAANLGK 85 (210)
Q Consensus 31 ~~~~~~~d~d~~~~f~CP~C~e-~~d~~~L~~H~~~eH~~e~~~~vCPvC~~~v~~ 85 (210)
+|-|++ -+++-|.||-|.- +|...+= ----||.-.-.||.|...+-+
T Consensus 898 gITeVd---PL~phy~C~~C~~~ef~~~~~-----~~sG~Dlpdk~Cp~Cg~~~~k 945 (1437)
T PRK00448 898 GITEVN---PLPPHYVCPNCKYSEFFTDGS-----VGSGFDLPDKDCPKCGTKLKK 945 (1437)
T ss_pred cCCCcC---CCCccccCccccccccccccc-----ccccccCccccCccccccccc
Confidence 444553 4889999999954 6643331 112456667789999997544
No 216
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=20.23 E-value=34 Score=35.92 Aligned_cols=9 Identities=33% Similarity=0.552 Sum_probs=0.0
Q ss_pred cccCCCCCc
Q 028361 44 CFPCPFCYL 52 (210)
Q Consensus 44 ~f~CP~C~e 52 (210)
.+.||-|+.
T Consensus 655 ~r~Cp~Cg~ 663 (900)
T PF03833_consen 655 RRRCPKCGK 663 (900)
T ss_dssp ---------
T ss_pred cccCcccCC
Confidence 455555544
Done!