Query 028603
Match_columns 206
No_of_seqs 151 out of 192
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 14:05:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028603.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028603hhsearch_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 6.9E-24 1.5E-28 165.4 4.3 78 119-198 1-78 (105)
2 PF05605 zf-Di19: Drought indu 99.8 4.1E-20 8.9E-25 127.3 4.4 54 45-98 1-54 (54)
3 KOG1280 Uncharacterized conser 98.6 7.4E-08 1.6E-12 89.3 6.1 71 26-98 60-141 (381)
4 KOG2923 Uncharacterized conser 94.8 0.017 3.6E-07 42.5 1.8 46 31-85 6-54 (67)
5 COG5216 Uncharacterized conser 94.7 0.014 3E-07 42.6 1.0 35 42-85 18-54 (67)
6 PF13894 zf-C2H2_4: C2H2-type 94.3 0.033 7.2E-07 30.6 1.8 23 47-69 1-24 (24)
7 PF09237 GAGA: GAGA factor; I 93.8 0.037 8E-07 39.3 1.6 27 73-99 22-50 (54)
8 PF13913 zf-C2HC_2: zinc-finge 92.4 0.12 2.6E-06 30.7 2.2 21 46-66 2-22 (25)
9 PLN03086 PRLI-interacting fact 92.1 0.17 3.8E-06 50.1 4.2 50 43-97 450-500 (567)
10 PF00096 zf-C2H2: Zinc finger, 91.6 0.1 2.2E-06 29.3 1.2 21 47-67 1-22 (23)
11 PHA00732 hypothetical protein 89.8 0.38 8.2E-06 35.9 3.2 42 47-93 2-44 (79)
12 PF12756 zf-C2H2_2: C2H2 type 89.7 0.17 3.7E-06 36.3 1.2 49 48-96 1-73 (100)
13 smart00531 TFIIE Transcription 89.1 0.32 7E-06 39.5 2.6 39 42-85 95-133 (147)
14 PF08271 TF_Zn_Ribbon: TFIIB z 88.7 0.16 3.6E-06 33.3 0.5 34 47-90 1-34 (43)
15 PF13909 zf-H2C2_5: C2H2-type 87.9 0.35 7.5E-06 27.6 1.5 24 47-70 1-24 (24)
16 PHA00733 hypothetical protein 87.5 0.82 1.8E-05 36.7 3.9 50 45-98 72-124 (128)
17 PLN03208 E3 ubiquitin-protein 87.3 0.24 5.3E-06 43.0 0.8 45 44-88 16-81 (193)
18 PF14354 Lar_restr_allev: Rest 86.6 0.16 3.5E-06 35.0 -0.6 31 46-83 3-37 (61)
19 PRK09710 lar restriction allev 86.3 0.27 5.9E-06 36.0 0.5 30 46-84 6-36 (64)
20 TIGR01206 lysW lysine biosynth 85.8 0.26 5.6E-06 34.8 0.2 30 46-84 2-31 (54)
21 PLN03086 PRLI-interacting fact 85.0 0.83 1.8E-05 45.4 3.3 38 45-85 477-514 (567)
22 PHA02768 hypothetical protein; 83.9 1.1 2.3E-05 31.9 2.6 34 46-83 5-39 (55)
23 COG5236 Uncharacterized conser 83.7 1.2 2.7E-05 42.6 3.6 56 43-104 217-312 (493)
24 smart00834 CxxC_CXXC_SSSS Puta 83.2 0.24 5.2E-06 31.3 -0.9 33 45-85 4-36 (41)
25 TIGR02098 MJ0042_CXXC MJ0042 f 81.9 0.98 2.1E-05 28.5 1.6 32 47-84 3-34 (38)
26 KOG2462 C2H2-type Zn-finger pr 81.8 1.3 2.9E-05 40.5 3.0 37 44-84 159-196 (279)
27 smart00504 Ubox Modified RING 81.2 1.8 4E-05 29.2 2.9 27 53-86 20-46 (63)
28 PF12756 zf-C2H2_2: C2H2 type 80.7 1 2.2E-05 32.2 1.6 27 45-71 49-76 (100)
29 smart00734 ZnF_Rad18 Rad18-lik 79.8 1.7 3.7E-05 26.1 2.1 20 47-66 2-21 (26)
30 PRK14892 putative transcriptio 79.7 0.66 1.4E-05 36.4 0.3 34 44-86 19-53 (99)
31 PF09986 DUF2225: Uncharacteri 79.6 0.42 9.1E-06 41.3 -0.9 17 46-62 5-21 (214)
32 PF08274 PhnA_Zn_Ribbon: PhnA 78.2 0.71 1.5E-05 29.0 0.1 25 47-83 3-27 (30)
33 KOG2462 C2H2-type Zn-finger pr 77.5 2.4 5.3E-05 38.9 3.3 84 46-137 187-273 (279)
34 TIGR02605 CxxC_CxxC_SSSS putat 76.5 1 2.3E-05 30.0 0.5 31 45-83 4-34 (52)
35 PF14255 Cys_rich_CPXG: Cystei 76.5 0.77 1.7E-05 32.1 -0.1 12 47-58 1-12 (52)
36 KOG1842 FYVE finger-containing 76.4 1.6 3.5E-05 42.6 2.0 35 41-75 10-45 (505)
37 PF14206 Cys_rich_CPCC: Cystei 76.1 1.2 2.5E-05 33.7 0.7 27 46-83 1-28 (78)
38 COG1655 Uncharacterized protei 75.5 1.1 2.3E-05 40.6 0.5 13 45-57 18-30 (267)
39 smart00355 ZnF_C2H2 zinc finge 74.3 4.3 9.2E-05 21.9 2.6 23 47-70 1-24 (26)
40 PF04564 U-box: U-box domain; 72.7 3.1 6.7E-05 29.9 2.2 37 44-86 2-50 (73)
41 PHA00616 hypothetical protein 72.3 2.5 5.4E-05 28.8 1.6 25 47-71 2-27 (44)
42 cd00350 rubredoxin_like Rubred 72.2 1.3 2.8E-05 27.7 0.1 10 74-83 16-25 (33)
43 KOG3623 Homeobox transcription 71.9 1.6 3.4E-05 45.2 0.7 42 44-85 208-250 (1007)
44 PRK00398 rpoP DNA-directed RNA 71.6 2 4.4E-05 28.4 1.0 28 46-84 3-30 (46)
45 PF05129 Elf1: Transcription e 70.7 1.8 3.9E-05 32.5 0.6 34 44-84 20-55 (81)
46 PF03470 zf-XS: XS zinc finger 70.6 3.1 6.7E-05 28.3 1.7 9 56-64 12-20 (43)
47 PF05605 zf-Di19: Drought indu 69.2 4.3 9.4E-05 27.5 2.2 24 46-70 31-54 (54)
48 PTZ00255 60S ribosomal protein 69.0 1.5 3.2E-05 34.0 -0.1 33 41-85 31-64 (90)
49 PRK14890 putative Zn-ribbon RN 68.3 4 8.6E-05 29.5 2.0 34 42-82 21-55 (59)
50 TIGR03655 anti_R_Lar restricti 68.2 2.3 4.9E-05 29.1 0.7 30 48-84 3-35 (53)
51 PRK12495 hypothetical protein; 65.8 3.8 8.1E-05 36.6 1.7 29 45-86 41-69 (226)
52 PRK06266 transcription initiat 65.8 4.4 9.4E-05 34.4 2.1 34 42-85 113-146 (178)
53 PF13912 zf-C2H2_6: C2H2-type 65.7 3.6 7.8E-05 23.6 1.1 23 47-69 2-25 (27)
54 cd00729 rubredoxin_SM Rubredox 65.6 2.1 4.6E-05 27.2 0.1 26 46-84 2-27 (34)
55 TIGR00373 conserved hypothetic 65.3 4.7 0.0001 33.4 2.1 34 42-85 105-138 (158)
56 PF02176 zf-TRAF: TRAF-type zi 64.6 2.4 5.3E-05 28.6 0.3 45 46-92 9-60 (60)
57 KOG2593 Transcription initiati 63.9 5.1 0.00011 38.9 2.3 63 34-103 116-192 (436)
58 TIGR00280 L37a ribosomal prote 62.6 2.1 4.6E-05 33.3 -0.4 17 41-57 30-47 (91)
59 COG5175 MOT2 Transcriptional r 61.9 5.3 0.00011 38.3 2.0 35 49-84 17-62 (480)
60 PF04780 DUF629: Protein of un 61.5 6.7 0.00015 38.3 2.7 42 43-84 54-99 (466)
61 cd00730 rubredoxin Rubredoxin; 61.4 5.8 0.00012 27.4 1.7 14 41-54 29-42 (50)
62 PF12773 DZR: Double zinc ribb 61.1 4.2 9.2E-05 26.8 0.9 28 47-86 13-40 (50)
63 PF00301 Rubredoxin: Rubredoxi 60.5 4.2 9.2E-05 27.8 0.9 14 41-54 29-42 (47)
64 PRK03976 rpl37ae 50S ribosomal 60.1 2.6 5.6E-05 32.7 -0.3 17 41-57 31-48 (90)
65 PF11789 zf-Nse: Zinc-finger o 59.3 8.4 0.00018 27.0 2.2 33 43-80 8-53 (57)
66 PF13395 HNH_4: HNH endonuclea 59.0 5.2 0.00011 27.3 1.1 14 49-62 1-14 (54)
67 COG4888 Uncharacterized Zn rib 58.9 4.3 9.2E-05 32.4 0.7 36 44-84 20-55 (104)
68 PF07754 DUF1610: Domain of un 58.2 5.5 0.00012 24.0 1.0 12 43-54 13-24 (24)
69 PRK00420 hypothetical protein; 58.1 7.7 0.00017 31.1 2.1 27 47-85 24-50 (112)
70 smart00659 RPOLCX RNA polymera 57.2 5.4 0.00012 26.8 0.9 28 46-85 2-29 (44)
71 KOG2932 E3 ubiquitin ligase in 54.6 5.8 0.00012 37.5 1.0 58 46-103 90-177 (389)
72 PF15616 TerY-C: TerY-C metal 54.5 3.3 7.2E-05 34.0 -0.5 44 44-89 75-119 (131)
73 COG4311 SoxD Sarcosine oxidase 53.4 6 0.00013 31.2 0.7 9 46-54 3-11 (97)
74 PF09723 Zn-ribbon_8: Zinc rib 53.2 3.1 6.8E-05 27.3 -0.7 31 45-83 4-34 (42)
75 KOG0320 Predicted E3 ubiquitin 52.8 12 0.00027 32.6 2.6 43 45-87 130-179 (187)
76 COG0675 Transposase and inacti 52.7 11 0.00024 32.1 2.3 45 33-93 296-340 (364)
77 COG2888 Predicted Zn-ribbon RN 52.5 13 0.00028 27.1 2.3 35 41-82 22-57 (61)
78 PF10571 UPF0547: Uncharacteri 52.1 8.6 0.00019 23.3 1.1 8 49-56 3-10 (26)
79 PF14446 Prok-RING_1: Prokaryo 50.4 12 0.00025 26.6 1.8 27 46-85 5-31 (54)
80 PF07282 OrfB_Zn_ribbon: Putat 49.9 19 0.00041 25.0 2.8 38 42-91 24-62 (69)
81 PF14634 zf-RING_5: zinc-RING 49.0 14 0.0003 23.9 1.8 20 61-82 24-43 (44)
82 PF01780 Ribosomal_L37ae: Ribo 48.3 7.1 0.00015 30.3 0.4 14 41-54 30-43 (90)
83 PRK03922 hypothetical protein; 48.1 8.9 0.00019 31.0 1.0 13 46-58 49-61 (113)
84 TIGR00100 hypA hydrogenase nic 47.9 4.9 0.00011 31.6 -0.5 30 42-84 66-95 (115)
85 PF14616 DUF4451: Domain of un 47.8 12 0.00025 30.1 1.6 28 75-102 25-57 (124)
86 PF04475 DUF555: Protein of un 47.3 9.3 0.0002 30.4 1.0 13 46-58 47-59 (102)
87 PF03145 Sina: Seven in absent 47.1 9 0.00019 32.1 0.9 54 45-101 13-75 (198)
88 PRK12496 hypothetical protein; 45.6 14 0.00031 30.8 1.9 28 46-86 127-154 (164)
89 PF13248 zf-ribbon_3: zinc-rib 45.5 13 0.00028 22.0 1.2 9 48-56 4-12 (26)
90 PF04981 NMD3: NMD3 family ; 45.3 14 0.0003 32.2 1.8 36 49-84 1-44 (236)
91 TIGR00570 cdk7 CDK-activating 45.1 14 0.0003 34.4 1.9 39 46-85 3-53 (309)
92 PF13465 zf-H2C2_2: Zinc-finge 44.8 21 0.00045 20.9 2.0 22 60-83 1-22 (26)
93 PF10058 DUF2296: Predicted in 43.7 10 0.00022 26.5 0.6 9 46-54 44-52 (54)
94 COG1592 Rubrerythrin [Energy p 42.7 13 0.00028 31.7 1.2 25 46-84 134-158 (166)
95 KOG3608 Zn finger proteins [Ge 42.6 29 0.00062 33.7 3.6 48 46-94 263-313 (467)
96 smart00451 ZnF_U1 U1-like zinc 42.6 20 0.00043 21.5 1.7 22 46-67 3-25 (35)
97 PRK11595 DNA utilization prote 42.6 12 0.00027 32.1 1.1 34 48-83 7-42 (227)
98 PF08996 zf-DNA_Pol: DNA Polym 42.6 3.1 6.7E-05 35.2 -2.6 40 44-85 16-55 (188)
99 PF09538 FYDLN_acid: Protein o 42.5 15 0.00032 29.1 1.4 33 42-87 5-38 (108)
100 PF09862 DUF2089: Protein of u 42.1 4.4 9.5E-05 32.6 -1.6 40 49-103 1-55 (113)
101 TIGR00686 phnA alkylphosphonat 41.5 12 0.00025 30.2 0.7 26 47-84 3-28 (109)
102 PRK11088 rrmA 23S rRNA methylt 41.1 5.8 0.00013 34.5 -1.1 26 46-73 2-29 (272)
103 PF13719 zinc_ribbon_5: zinc-r 41.0 25 0.00054 22.4 2.1 31 47-83 3-33 (37)
104 KOG2177 Predicted E3 ubiquitin 40.7 11 0.00024 30.4 0.4 36 45-82 12-54 (386)
105 PRK00423 tfb transcription ini 40.7 19 0.0004 32.7 2.0 40 43-93 8-48 (310)
106 PF02892 zf-BED: BED zinc fing 40.4 21 0.00044 22.8 1.6 24 74-97 15-44 (45)
107 smart00507 HNHc HNH nucleases. 40.0 4.4 9.6E-05 25.3 -1.6 21 47-67 11-31 (52)
108 PF13824 zf-Mss51: Zinc-finger 39.8 15 0.00033 26.2 1.0 22 43-71 11-32 (55)
109 PRK12380 hydrogenase nickel in 39.4 9 0.0002 30.1 -0.2 30 42-84 66-95 (113)
110 PF02146 SIR2: Sir2 family; I 39.2 11 0.00024 30.8 0.3 40 46-90 105-144 (178)
111 PF12171 zf-C2H2_jaz: Zinc-fin 37.1 21 0.00045 20.7 1.2 20 47-66 2-22 (27)
112 PF04423 Rad50_zn_hook: Rad50 37.0 14 0.0003 25.1 0.4 14 48-61 22-35 (54)
113 KOG0402 60S ribosomal protein 36.9 11 0.00024 29.4 -0.1 16 42-57 32-48 (92)
114 COG1997 RPL43A Ribosomal prote 36.9 7.5 0.00016 30.3 -1.0 33 40-84 29-62 (89)
115 COG1499 NMD3 NMD protein affec 36.8 18 0.00039 34.1 1.3 40 44-83 4-51 (355)
116 PRK03824 hypA hydrogenase nick 36.6 10 0.00022 30.7 -0.3 18 42-59 66-83 (135)
117 smart00614 ZnF_BED BED zinc fi 36.3 19 0.00042 24.0 1.1 26 45-70 17-48 (50)
118 PF03966 Trm112p: Trm112p-like 36.1 25 0.00054 24.9 1.7 38 46-83 7-61 (68)
119 PF06957 COPI_C: Coatomer (COP 36.0 13 0.00028 35.9 0.2 34 45-91 379-413 (422)
120 PF00097 zf-C3HC4: Zinc finger 35.9 16 0.00035 22.7 0.6 9 73-81 33-41 (41)
121 KOG2879 Predicted E3 ubiquitin 35.8 10 0.00022 35.1 -0.5 41 45-85 238-286 (298)
122 PF14279 HNH_5: HNH endonuclea 35.7 8.5 0.00018 28.2 -0.8 35 49-88 1-43 (71)
123 PF08209 Sgf11: Sgf11 (transcr 35.6 28 0.00061 22.3 1.7 21 74-94 3-24 (33)
124 PF14353 CpXC: CpXC protein 35.4 16 0.00034 28.5 0.6 29 45-77 37-65 (128)
125 PF12760 Zn_Tnp_IS1595: Transp 35.1 22 0.00048 23.4 1.2 10 45-54 17-26 (46)
126 PHA02929 N1R/p28-like protein; 35.0 7.1 0.00015 34.9 -1.6 43 44-86 172-227 (238)
127 TIGR00373 conserved hypothetic 34.9 28 0.0006 28.8 2.0 21 45-65 127-150 (158)
128 PF05207 zf-CSL: CSL zinc fing 33.9 13 0.00027 25.9 -0.2 45 33-86 4-51 (55)
129 PF12230 PRP21_like_P: Pre-mRN 33.6 14 0.0003 31.8 0.0 22 75-96 168-190 (229)
130 smart00661 RPOL9 RNA polymeras 33.6 17 0.00037 23.8 0.5 10 75-84 20-29 (52)
131 PF11672 DUF3268: Protein of u 33.3 16 0.00034 28.9 0.3 38 47-87 3-43 (102)
132 TIGR01374 soxD sarcosine oxida 33.3 19 0.00041 27.6 0.7 8 47-54 2-9 (84)
133 COG1198 PriA Primosomal protei 33.2 14 0.00029 38.1 -0.2 41 42-84 440-484 (730)
134 PF12660 zf-TFIIIC: Putative z 33.0 7.6 0.00017 29.9 -1.5 38 48-85 16-65 (99)
135 KOG1493 Anaphase-promoting com 32.9 36 0.00078 26.2 2.1 36 47-83 32-78 (84)
136 KOG4628 Predicted E3 ubiquitin 32.9 9 0.00019 36.2 -1.4 39 47-85 230-277 (348)
137 PF04780 DUF629: Protein of un 32.8 19 0.00042 35.2 0.9 48 55-102 20-86 (466)
138 COG4049 Uncharacterized protei 32.7 22 0.00048 25.9 0.9 26 76-101 18-45 (65)
139 PHA00733 hypothetical protein 32.2 44 0.00096 26.8 2.7 25 46-70 99-124 (128)
140 cd03019 DsbA_DsbA DsbA family, 32.2 19 0.00041 28.2 0.6 19 45-63 23-42 (178)
141 PF12230 PRP21_like_P: Pre-mRN 31.9 15 0.00033 31.6 0.0 23 46-68 168-190 (229)
142 COG4391 Uncharacterized protei 31.6 25 0.00053 25.8 1.0 13 72-84 45-57 (62)
143 COG5189 SFP1 Putative transcri 31.5 25 0.00054 33.6 1.3 40 46-85 349-408 (423)
144 PF01155 HypA: Hydrogenase exp 31.4 6.1 0.00013 30.9 -2.3 30 42-84 66-95 (113)
145 PF05876 Terminase_GpA: Phage 31.4 22 0.00047 35.0 0.9 42 44-87 198-241 (557)
146 TIGR00599 rad18 DNA repair pro 31.0 23 0.00049 34.0 0.9 50 41-92 21-77 (397)
147 PRK10220 hypothetical protein; 31.0 33 0.00072 27.7 1.7 12 73-84 18-29 (111)
148 PRK04023 DNA polymerase II lar 30.8 21 0.00046 38.3 0.8 37 45-85 637-673 (1121)
149 KOG1002 Nucleotide excision re 30.4 26 0.00056 35.6 1.3 54 40-93 530-593 (791)
150 TIGR02300 FYDLN_acid conserved 30.3 32 0.00069 28.5 1.6 32 42-86 5-37 (129)
151 PRK06266 transcription initiat 30.0 38 0.00082 28.7 2.0 19 45-63 135-156 (178)
152 PF09706 Cas_CXXC_CXXC: CRISPR 29.9 17 0.00038 26.3 -0.0 11 44-54 3-13 (69)
153 PF12013 DUF3505: Protein of u 29.2 43 0.00094 25.4 2.1 30 71-100 7-37 (109)
154 PF13462 Thioredoxin_4: Thiore 29.1 6.2 0.00013 30.4 -2.6 21 45-65 20-41 (162)
155 PF14968 CCDC84: Coiled coil p 28.7 28 0.0006 32.8 1.1 26 41-66 53-85 (336)
156 KOG0823 Predicted E3 ubiquitin 28.7 16 0.00036 32.7 -0.4 45 44-89 45-98 (230)
157 PF04267 SoxD: Sarcosine oxida 28.2 15 0.00033 28.1 -0.6 7 48-54 3-9 (84)
158 KOG2231 Predicted E3 ubiquitin 28.1 38 0.00082 34.7 2.0 30 43-72 179-209 (669)
159 PF12861 zf-Apc11: Anaphase-pr 27.9 25 0.00054 27.1 0.5 37 48-84 34-80 (85)
160 KOG4696 Uncharacterized conser 27.8 38 0.00083 32.1 1.8 24 46-70 2-25 (393)
161 PF11290 DUF3090: Protein of u 27.4 31 0.00068 29.7 1.1 13 47-59 155-167 (171)
162 KOG3940 Uncharacterized conser 27.4 37 0.0008 32.1 1.6 24 41-64 15-38 (351)
163 COG1656 Uncharacterized conser 27.2 45 0.00098 28.6 2.0 41 47-87 98-144 (165)
164 PF14369 zf-RING_3: zinc-finge 27.0 30 0.00066 22.1 0.8 9 48-56 23-31 (35)
165 PRK05477 gatB aspartyl/glutamy 26.7 22 0.00048 34.8 0.1 18 69-86 31-48 (474)
166 PF10276 zf-CHCC: Zinc-finger 26.6 23 0.0005 23.5 0.2 9 46-54 29-37 (40)
167 PRK09678 DNA-binding transcrip 26.3 32 0.00068 25.6 0.8 8 47-54 2-9 (72)
168 COG1675 TFA1 Transcription ini 26.1 50 0.0011 28.4 2.1 32 44-85 111-142 (176)
169 PF13717 zinc_ribbon_4: zinc-r 26.1 60 0.0013 20.6 2.0 31 47-83 3-33 (36)
170 PRK05452 anaerobic nitric oxid 25.8 38 0.00082 32.6 1.5 12 43-54 422-433 (479)
171 PF12874 zf-met: Zinc-finger o 25.5 40 0.00088 18.7 1.0 7 78-84 3-9 (25)
172 PF10023 DUF2265: Predicted am 25.5 29 0.00064 32.7 0.7 35 124-162 125-159 (337)
173 PF14311 DUF4379: Domain of un 25.5 37 0.0008 23.0 1.0 33 41-81 23-55 (55)
174 PRK00564 hypA hydrogenase nick 25.4 21 0.00046 28.2 -0.3 31 42-84 67-97 (117)
175 cd02972 DsbA_family DsbA famil 25.1 21 0.00045 24.3 -0.3 17 46-62 6-23 (98)
176 PF09334 tRNA-synt_1g: tRNA sy 24.9 14 0.0003 34.6 -1.6 40 46-85 136-176 (391)
177 KOG3608 Zn finger proteins [Ge 24.3 56 0.0012 31.7 2.3 43 60-102 336-381 (467)
178 COG1405 SUA7 Transcription ini 24.1 46 0.00099 30.4 1.6 43 47-99 2-44 (285)
179 TIGR03830 CxxCG_CxxCG_HTH puta 23.9 18 0.00039 27.5 -0.9 37 49-85 1-41 (127)
180 PRK14714 DNA polymerase II lar 23.6 30 0.00064 38.0 0.4 35 46-85 667-702 (1337)
181 PRK03681 hypA hydrogenase nick 23.5 25 0.00053 27.7 -0.2 11 44-54 68-78 (114)
182 PRK00464 nrdR transcriptional 23.1 36 0.00078 28.5 0.7 32 47-84 1-37 (154)
183 PLN02751 glutamyl-tRNA(Gln) am 22.9 28 0.00061 34.7 0.1 21 66-86 84-104 (544)
184 PHA02565 49 recombination endo 22.6 26 0.00057 29.8 -0.2 41 46-86 20-66 (157)
185 COG5415 Predicted integral mem 22.4 66 0.0014 29.1 2.2 35 43-86 189-225 (251)
186 KOG2817 Predicted E3 ubiquitin 22.4 46 0.001 32.1 1.3 16 44-59 372-387 (394)
187 PHA02540 61 DNA primase; Provi 22.3 38 0.00082 31.8 0.7 10 45-54 26-35 (337)
188 cd03024 DsbA_FrnE DsbA family, 21.9 23 0.00049 28.6 -0.7 22 44-65 4-26 (201)
189 PRK05654 acetyl-CoA carboxylas 21.4 51 0.0011 30.1 1.4 29 46-84 27-55 (292)
190 TIGR00133 gatB glutamyl-tRNA(G 20.9 33 0.00072 33.6 0.1 15 72-86 34-48 (478)
191 PF11793 FANCL_C: FANCL C-term 20.9 58 0.0013 23.4 1.3 46 42-87 16-67 (70)
192 PF03604 DNA_RNApol_7kD: DNA d 20.8 60 0.0013 20.5 1.2 13 42-54 13-25 (32)
193 COG1885 Uncharacterized protei 20.8 48 0.001 26.8 0.9 14 46-59 49-62 (115)
194 TIGR00515 accD acetyl-CoA carb 20.6 58 0.0013 29.7 1.6 29 46-84 26-54 (285)
195 PF13453 zf-TFIIB: Transcripti 20.6 28 0.00061 22.4 -0.3 9 49-57 2-10 (41)
196 COG3058 FdhE Uncharacterized p 20.6 33 0.00072 32.0 0.0 18 74-91 184-201 (308)
197 KOG4727 U1-like Zn-finger prot 20.6 43 0.00094 29.3 0.7 19 77-95 77-97 (193)
198 KOG2482 Predicted C2H2-type Zn 20.4 48 0.0011 31.9 1.0 32 45-76 278-310 (423)
199 cd03021 DsbA_GSTK DsbA family, 20.2 17 0.00038 30.3 -1.8 13 43-55 5-17 (209)
200 COG5574 PEX10 RING-finger-cont 20.1 24 0.00053 32.4 -1.0 42 45-86 214-262 (271)
201 PF12013 DUF3505: Protein of u 20.1 78 0.0017 24.0 2.0 26 45-70 79-109 (109)
202 cd03023 DsbA_Com1_like DsbA fa 20.0 36 0.00078 25.6 0.1 9 46-54 14-22 (154)
No 1
>PF14571 Di19_C: Stress-induced protein Di19, C-terminal
Probab=99.89 E-value=6.9e-24 Score=165.36 Aligned_cols=78 Identities=53% Similarity=0.674 Sum_probs=71.3
Q ss_pred hHhhhchhhhhhhhhhhhCCCCCCCCCCCCCCCCCCchhhhhccCCCCCchhhhcccccCccccccccccCCcCCccccc
Q 028603 119 ALSLLGRDLREAHLQVLLGGSGYRSSNANISNAATDPFLSSLILNFPSSEAEEISKSVVTSTEDTSAKSAAPTHMWKTRY 198 (206)
Q Consensus 119 ~ls~l~k~lre~~lq~llgg~~~~~~~~~~s~~~pDPLLSsFi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~ 198 (206)
|||+|+|||||||||+||||+ ++++++++|++|||||||||||+|.++.++.+++..++.++++.++..+.+.|++++
T Consensus 1 tlsll~kelre~~LQsllGgs--~~~~~~ssn~apDPLLSSFI~n~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~s~ 78 (105)
T PF14571_consen 1 TLSLLRKELREGYLQSLLGGS--RSSSSSSSNSAPDPLLSSFICNFPAPEAEEPSKSSSSSEEKKSSKKSSSEQNVKSSA 78 (105)
T ss_pred CcchhhhhhhhhhhhhhcCCC--cCCCCCCCCCCCcHHHHHHhcCCCCccccccCCccccccccccccccchhccccccc
Confidence 689999999999999999998 455678999999999999999999999999999888888899999999999999765
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=99.80 E-value=4.1e-20 Score=127.27 Aligned_cols=54 Identities=48% Similarity=0.938 Sum_probs=52.2
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccchhhhHhhhhhcccc
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHG 98 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~d~l~HL~~qH~ 98 (206)
++|+||||+++||+.+|++|++++|..+.++||||||+.+++.||++||+.+|+
T Consensus 1 ~~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~~l~~Hl~~~H~ 54 (54)
T PF05605_consen 1 DSFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSRVTDNLIRHLNSQHR 54 (54)
T ss_pred CCcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhhhhhHHHHHHHHhcC
Confidence 379999999999999999999999999999999999999999999999999996
No 3
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=98.59 E-value=7.4e-08 Score=89.26 Aligned_cols=71 Identities=21% Similarity=0.445 Sum_probs=55.3
Q ss_pred cccccc-cCCCCCCCCCCCCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccch---------hhhHhhhhh
Q 028603 26 SSQIDR-LSIDDFEVEDDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV---------ARDMLSHIT 94 (206)
Q Consensus 26 ~s~~~~-~~~d~~e~ddd~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v---------s~d~l~HL~ 94 (206)
+-++++ +|+|-+--+++ +.|+||||++ +|.+..+.+|+..+|+.....+|||||++.+ +.+...|+.
T Consensus 60 ~~dfeL~f~Ge~i~~y~~--qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~~~qp~~~~~~~~~~~~~~ 137 (381)
T KOG1280|consen 60 RVDFELYFGGEPISHYDP--QSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANPEMQPIHSKETENLSVHWT 137 (381)
T ss_pred ccceeeEecCcccccccc--ccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCcccCchhhhhhhhhhhhhh
Confidence 345554 67676654443 3999999999 9999999999999999999999999999985 345556665
Q ss_pred cccc
Q 028603 95 LQHG 98 (206)
Q Consensus 95 ~qH~ 98 (206)
..|-
T Consensus 138 ~~a~ 141 (381)
T KOG1280|consen 138 EIAL 141 (381)
T ss_pred hhcc
Confidence 5553
No 4
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.85 E-value=0.017 Score=42.52 Aligned_cols=46 Identities=33% Similarity=0.757 Sum_probs=31.1
Q ss_pred ccCCCCCC-CCCCCCCcccCCCCCC--CCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 31 RLSIDDFE-VEDDVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 31 ~~~~d~~e-~ddd~r~~F~CPfC~e--~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
-..++|++ .++...-+|+|| ||. .+....|. ..-..+.||-|+-.+
T Consensus 6 eVeiedfe~~~e~~~y~yPCp-CGDrf~It~edL~--------~ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 6 EVEIEDFEFDEENQTYYYPCP-CGDRFQITLEDLE--------NGEDVARCPSCSLII 54 (67)
T ss_pred eEEeecceeccCCCeEEcCCC-CCCeeeecHHHHh--------CCCeeecCCCceEEE
Confidence 34567776 344556789999 998 44444442 334568999999876
No 5
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=94.69 E-value=0.014 Score=42.63 Aligned_cols=35 Identities=31% Similarity=0.765 Sum_probs=25.0
Q ss_pred CCCCcccCCCCCC--CCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 42 DVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 42 d~r~~F~CPfC~e--~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
+..-+|+|| ||. ++.+..|. ..-..++||-|+-+|
T Consensus 18 ~~~ftyPCP-CGDRFeIsLeDl~--------~GE~VArCPSCSLiv 54 (67)
T COG5216 18 EKTFTYPCP-CGDRFEISLEDLR--------NGEVVARCPSCSLIV 54 (67)
T ss_pred CceEEecCC-CCCEeEEEHHHhh--------CCceEEEcCCceEEE
Confidence 345689999 988 55555553 344568999999876
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=94.31 E-value=0.033 Score=30.60 Aligned_cols=23 Identities=30% Similarity=0.631 Sum_probs=17.4
Q ss_pred ccCCCCCC-CCCHHHHHHHhhhhc
Q 028603 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (206)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~eeH 69 (206)
|.||+|+. --+..+|..|+...|
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 68999999 777888999988776
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=93.76 E-value=0.037 Score=39.25 Aligned_cols=27 Identities=26% Similarity=0.738 Sum_probs=19.0
Q ss_pred CCceecCccccch--hhhHhhhhhccccc
Q 028603 73 SKVTVCPICSVKV--ARDMLSHITLQHGH 99 (206)
Q Consensus 73 ~k~vVCPICa~~v--s~d~l~HL~~qH~~ 99 (206)
.....||+|.+.+ ++|+-+||-+.|+.
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~ 50 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFK 50 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTT
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcc
Confidence 3457999999986 78999999999975
No 8
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.38 E-value=0.12 Score=30.75 Aligned_cols=21 Identities=33% Similarity=0.668 Sum_probs=18.9
Q ss_pred cccCCCCCCCCCHHHHHHHhh
Q 028603 46 DFPCPYCYEDFDIASLCSHLE 66 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~ 66 (206)
..+||+||..|....|-.|..
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHH
Confidence 578999999999999999974
No 9
>PLN03086 PRLI-interacting factor K; Provisional
Probab=92.10 E-value=0.17 Score=50.06 Aligned_cols=50 Identities=22% Similarity=0.497 Sum_probs=39.0
Q ss_pred CCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch-hhhHhhhhhccc
Q 028603 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV-ARDMLSHITLQH 97 (206)
Q Consensus 43 ~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v-s~d~l~HL~~qH 97 (206)
+..-+.||+|++.|....|-.|....| +.+.|| |...+ ..+|..|++...
T Consensus 450 l~~H~~C~~Cgk~f~~s~LekH~~~~H----kpv~Cp-Cg~~~~R~~L~~H~~thC 500 (567)
T PLN03086 450 AKNHVHCEKCGQAFQQGEMEKHMKVFH----EPLQCP-CGVVLEKEQMVQHQASTC 500 (567)
T ss_pred cccCccCCCCCCccchHHHHHHHHhcC----CCccCC-CCCCcchhHHHhhhhccC
Confidence 334579999999999999999999866 678999 96543 568888876533
No 10
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=91.60 E-value=0.1 Score=29.30 Aligned_cols=21 Identities=24% Similarity=0.550 Sum_probs=15.9
Q ss_pred ccCCCCCC-CCCHHHHHHHhhh
Q 028603 47 FPCPYCYE-DFDIASLCSHLED 67 (206)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~e 67 (206)
|.||.|++ =-+...|..|+..
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 67888888 5567778888765
No 11
>PHA00732 hypothetical protein
Probab=89.77 E-value=0.38 Score=35.94 Aligned_cols=42 Identities=29% Similarity=0.652 Sum_probs=31.9
Q ss_pred ccCCCCCCC-CCHHHHHHHhhhhccCCCCceecCccccchhhhHhhhh
Q 028603 47 FPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (206)
Q Consensus 47 F~CPfC~e~-fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~d~l~HL 93 (206)
|.|+.|++. -....|..|....|.. ..|++|...-. ++..|+
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~----~~C~~CgKsF~-~l~~H~ 44 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTL----TKCPVCNKSYR-RLNQHF 44 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCC----CccCCCCCEeC-Chhhhh
Confidence 789999994 4788899999866653 26999988654 466665
No 12
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=89.66 E-value=0.17 Score=36.30 Aligned_cols=49 Identities=20% Similarity=0.551 Sum_probs=15.0
Q ss_pred cCCCCCCC-CCHHHHHHHhhhhccCCCC---------------------ceecCccccch--hhhHhhhhhcc
Q 028603 48 PCPYCYED-FDIASLCSHLEDEHSCESK---------------------VTVCPICSVKV--ARDMLSHITLQ 96 (206)
Q Consensus 48 ~CPfC~e~-fD~~~L~~H~~eeH~~e~k---------------------~vVCPICa~~v--s~d~l~HL~~q 96 (206)
-|+||+.. -++..|..|+...|.+... .-.|++|.... ...+..||...
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 39999994 5688999999999987322 13499998875 45788999753
No 13
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.08 E-value=0.32 Score=39.51 Aligned_cols=39 Identities=18% Similarity=0.521 Sum_probs=27.0
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.....|.||.|+..|+..+-..... . ....+||.|-..+
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~d---~--~~~f~Cp~Cg~~l 133 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLLD---M--DGTFTCPRCGEEL 133 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhcC---C--CCcEECCCCCCEE
Confidence 3467999999999777655433222 1 3448999998876
No 14
>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=88.65 E-value=0.16 Score=33.26 Aligned_cols=34 Identities=29% Similarity=0.657 Sum_probs=21.6
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccchhhhHh
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~d~l 90 (206)
|.||.|+... + +.+ ......||+.|-..+..+.+
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 6899999832 1 111 44567899999887766554
No 15
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=87.86 E-value=0.35 Score=27.57 Aligned_cols=24 Identities=29% Similarity=0.635 Sum_probs=16.9
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhcc
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHS 70 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~ 70 (206)
|.|++|.-.-....|..|++..|.
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 679999883238889999988774
No 16
>PHA00733 hypothetical protein
Probab=87.49 E-value=0.82 Score=36.74 Aligned_cols=50 Identities=26% Similarity=0.618 Sum_probs=37.0
Q ss_pred CcccCCCCCCC-CCHHHHHHHhhhhccCCCCceecCccccch--hhhHhhhhhcccc
Q 028603 45 PDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQHG 98 (206)
Q Consensus 45 ~~F~CPfC~e~-fD~~~L~~H~~eeH~~e~k~vVCPICa~~v--s~d~l~HL~~qH~ 98 (206)
..|.|+.|+.. -....|..|... | .....|++|.... ..+|..|+.--|+
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 36999999995 456678888874 2 1346999997764 5688888887775
No 17
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=87.31 E-value=0.24 Score=43.05 Aligned_cols=45 Identities=24% Similarity=0.697 Sum_probs=28.3
Q ss_pred CCcccCCCCCCCCC--HHHHHHH-----hhhhccC--------------CCCceecCccccchhhh
Q 028603 44 RPDFPCPYCYEDFD--IASLCSH-----LEDEHSC--------------ESKVTVCPICSVKVARD 88 (206)
Q Consensus 44 r~~F~CPfC~e~fD--~~~L~~H-----~~eeH~~--------------e~k~vVCPICa~~vs~d 88 (206)
...|.||.|.+.+. +...|.| |-..... ..+...||+|...++.+
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~ 81 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEA 81 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChh
Confidence 45799999988332 3445666 3332211 23346899999998653
No 18
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=86.56 E-value=0.16 Score=34.98 Aligned_cols=31 Identities=26% Similarity=0.590 Sum_probs=19.7
Q ss_pred cccCCCCCC-CCCHHHHHHHhhhhccCCC---CceecCcccc
Q 028603 46 DFPCPYCYE-DFDIASLCSHLEDEHSCES---KVTVCPICSV 83 (206)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~---k~vVCPICa~ 83 (206)
.-+|||||. .+.+.. ....+. -.|.|..|-+
T Consensus 3 LkPCPFCG~~~~~~~~-------~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQ-------DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeec-------ccCCCCCCEEEEEcCCCCC
Confidence 468999997 554333 222222 4578999977
No 19
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=86.26 E-value=0.27 Score=36.00 Aligned_cols=30 Identities=20% Similarity=0.473 Sum_probs=20.9
Q ss_pred cccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
.=+|||||. .+.+. |....-.++|.-|-+.
T Consensus 6 lKPCPFCG~~~~~v~---------~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVK---------AISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEE---------ecCceEEEEcCCCCcC
Confidence 348999999 66554 2233335999999885
No 20
>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=85.79 E-value=0.26 Score=34.77 Aligned_cols=30 Identities=20% Similarity=0.686 Sum_probs=21.9
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
.|.||-||+.+++.... . .-.+.||.|-+.
T Consensus 2 ~~~CP~CG~~iev~~~~-------~--GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPE-------L--GELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCc-------c--CCEEeCCCCCCE
Confidence 58999999977654432 1 236899999886
No 21
>PLN03086 PRLI-interacting factor K; Provisional
Probab=85.02 E-value=0.83 Score=45.41 Aligned_cols=38 Identities=18% Similarity=0.467 Sum_probs=27.8
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
..+.|| ||..+....|..|.. .|+-. +...|+.|...+
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~-thCp~-Kpi~C~fC~~~v 514 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQA-STCPL-RLITCRFCGDMV 514 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhh-ccCCC-CceeCCCCCCcc
Confidence 457888 888778888888874 45543 667888887765
No 22
>PHA02768 hypothetical protein; Provisional
Probab=83.88 E-value=1.1 Score=31.94 Aligned_cols=34 Identities=26% Similarity=0.529 Sum_probs=25.3
Q ss_pred cccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCcccc
Q 028603 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
.|.||.||+ =...+.|..|... |. ++-.|..|..
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 488999999 5566789999988 44 4556777754
No 23
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=83.66 E-value=1.2 Score=42.58 Aligned_cols=56 Identities=27% Similarity=0.455 Sum_probs=44.2
Q ss_pred CCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccc-------------------------------h-----
Q 028603 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK-------------------------------V----- 85 (206)
Q Consensus 43 ~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~-------------------------------v----- 85 (206)
..---.|-||.. =+|-.+|..||.+.|- .|-||..+ +
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 455678999999 8899999999999985 56676554 0
Q ss_pred ---hhhHhhhhhccccchhhhh
Q 028603 86 ---ARDMLSHITLQHGHLFKLQ 104 (206)
Q Consensus 86 ---s~d~l~HL~~qH~~~~k~~ 104 (206)
-..++.||+..|+...+.+
T Consensus 291 f~~~~el~~h~~~~h~~~~~~~ 312 (493)
T COG5236 291 FPYHTELLEHLTRFHKVNARLS 312 (493)
T ss_pred eccHHHHHHHHHHHhhcccccC
Confidence 2368899999999988664
No 24
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=83.16 E-value=0.24 Score=31.30 Aligned_cols=33 Identities=21% Similarity=0.632 Sum_probs=21.9
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.+|.||-||..|++..-. .+...++||.|.+.+
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 368999999976643221 124567899998743
No 25
>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=81.93 E-value=0.98 Score=28.46 Aligned_cols=32 Identities=19% Similarity=0.520 Sum_probs=19.5
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
+.||.|+..|.+..- ....+...+.||.|-..
T Consensus 3 ~~CP~C~~~~~v~~~------~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDS------QLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHH------HcCCCCCEEECCCCCCE
Confidence 679999984444321 11223346889999654
No 26
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=81.85 E-value=1.3 Score=40.55 Aligned_cols=37 Identities=24% Similarity=0.584 Sum_probs=24.7
Q ss_pred CCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 44 r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
+..|.|++|++ -+.+..|--|+...= -.-+|+||-..
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~----l~c~C~iCGKa 196 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHT----LPCECGICGKA 196 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccC----CCccccccccc
Confidence 56788888888 788888888876531 23456666543
No 27
>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=81.19 E-value=1.8 Score=29.16 Aligned_cols=27 Identities=7% Similarity=0.113 Sum_probs=19.7
Q ss_pred CCCCCHHHHHHHhhhhccCCCCceecCccccchh
Q 028603 53 YEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 53 ~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs 86 (206)
|.-|+...+..++.. ...||+|...++
T Consensus 20 G~v~~~~~i~~~~~~-------~~~cP~~~~~~~ 46 (63)
T smart00504 20 GQTYERRAIEKWLLS-------HGTDPVTGQPLT 46 (63)
T ss_pred CCEEeHHHHHHHHHH-------CCCCCCCcCCCC
Confidence 445788888888865 358999987663
No 28
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=80.74 E-value=1 Score=32.18 Aligned_cols=27 Identities=33% Similarity=0.817 Sum_probs=21.6
Q ss_pred CcccCCCCCCCC-CHHHHHHHhhhhccC
Q 028603 45 PDFPCPYCYEDF-DIASLCSHLEDEHSC 71 (206)
Q Consensus 45 ~~F~CPfC~e~f-D~~~L~~H~~eeH~~ 71 (206)
..|.|++|++.| +...|..|+...+..
T Consensus 49 ~~~~C~~C~~~f~s~~~l~~Hm~~~~H~ 76 (100)
T PF12756_consen 49 ESFRCPYCNKTFRSREALQEHMRSKHHK 76 (100)
T ss_dssp SSEEBSSSS-EESSHHHHHHHHHHTTTT
T ss_pred CCCCCCccCCCCcCHHHHHHHHcCccCC
Confidence 369999999955 899999999987543
No 29
>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=79.83 E-value=1.7 Score=26.11 Aligned_cols=20 Identities=30% Similarity=0.796 Sum_probs=12.6
Q ss_pred ccCCCCCCCCCHHHHHHHhh
Q 028603 47 FPCPYCYEDFDIASLCSHLE 66 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~ 66 (206)
..||.|++.+....+-.|++
T Consensus 2 v~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVPENLINSHLD 21 (26)
T ss_pred CcCCCCcCcccHHHHHHHHH
Confidence 35666666666666666665
No 30
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=79.69 E-value=0.66 Score=36.36 Aligned_cols=34 Identities=18% Similarity=0.489 Sum_probs=20.9
Q ss_pred CCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccchh
Q 028603 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 44 r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs 86 (206)
...|.||||++ -+.+. -.+ ..--++||+|-..-+
T Consensus 19 pt~f~CP~Cge~~v~v~-------~~k--~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 19 PKIFECPRCGKVSISVK-------IKK--NIAIITCGNCGLYTE 53 (99)
T ss_pred CcEeECCCCCCeEeeee-------cCC--CcceEECCCCCCccC
Confidence 45899999996 22111 111 233489999977643
No 31
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=79.61 E-value=0.42 Score=41.30 Aligned_cols=17 Identities=24% Similarity=0.729 Sum_probs=13.6
Q ss_pred cccCCCCCCCCCHHHHH
Q 028603 46 DFPCPYCYEDFDIASLC 62 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~ 62 (206)
+++||+|+..|....+.
T Consensus 5 ~~~CPvC~~~F~~~~vr 21 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVR 21 (214)
T ss_pred ceECCCCCCeeeeeEEE
Confidence 68999999988876443
No 32
>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=78.25 E-value=0.71 Score=29.03 Aligned_cols=25 Identities=28% Similarity=0.813 Sum_probs=12.7
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCcccc
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
-.||.|+.++.. .+....|||-|..
T Consensus 3 p~Cp~C~se~~y------------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTY------------EDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----E------------E-SSSEEETTTTE
T ss_pred CCCCCCCCccee------------ccCCEEeCCcccc
Confidence 369999885554 5667789999974
No 33
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=77.52 E-value=2.4 Score=38.87 Aligned_cols=84 Identities=26% Similarity=0.402 Sum_probs=52.0
Q ss_pred cccCCCCCCCCCHHHHH-HHhhhhccCCCCceecCccccch--hhhHhhhhhccccchhhhhhhccccccCCCCchhHhh
Q 028603 46 DFPCPYCYEDFDIASLC-SHLEDEHSCESKVTVCPICSVKV--ARDMLSHITLQHGHLFKLQRRRRLRRVAIPSSQALSL 122 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~-~H~~eeH~~e~k~vVCPICa~~v--s~d~l~HL~~qH~~~~k~~rrrr~rr~~~~~~s~ls~ 122 (206)
-+.|++||+-|+..=|. -|++ .|..| |.-.||.|..-- -.||-.||.. |+..=+-+ =.+.-|. -+-+|+
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiR-THTGE-KPF~C~hC~kAFADRSNLRAHmQT-HS~~K~~q-C~~C~Ks----Fsl~Sy 258 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIR-THTGE-KPFSCPHCGKAFADRSNLRAHMQT-HSDVKKHQ-CPRCGKS----FALKSY 258 (279)
T ss_pred CcccccccccccchHHhhcccc-cccCC-CCccCCcccchhcchHHHHHHHHh-hcCCcccc-CcchhhH----HHHHHH
Confidence 58999999999988654 4554 45544 567999998775 4599999975 44321111 1112221 245677
Q ss_pred hchhhhhhhhhhhhC
Q 028603 123 LGRDLREAHLQVLLG 137 (206)
Q Consensus 123 l~k~lre~~lq~llg 137 (206)
|.|-+..|=+..+.|
T Consensus 259 LnKH~ES~C~~~~~g 273 (279)
T KOG2462|consen 259 LNKHSESACLKYLAG 273 (279)
T ss_pred HHHhhhhcccccccc
Confidence 887775554444433
No 34
>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=76.47 E-value=1 Score=30.05 Aligned_cols=31 Identities=19% Similarity=0.712 Sum_probs=21.5
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCcccc
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
.+|.|+-||..|++.. ... +...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~---~~~-----~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQ---KMS-----DDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEE---ecC-----CCCCCCCCCCCC
Confidence 3699999999887431 111 135578999987
No 35
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=76.45 E-value=0.77 Score=32.13 Aligned_cols=12 Identities=50% Similarity=1.270 Sum_probs=9.1
Q ss_pred ccCCCCCCCCCH
Q 028603 47 FPCPYCYEDFDI 58 (206)
Q Consensus 47 F~CPfC~e~fD~ 58 (206)
+.|||||+.+++
T Consensus 1 i~CPyCge~~~~ 12 (52)
T PF14255_consen 1 IQCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCCeeEE
Confidence 479999995544
No 36
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=76.35 E-value=1.6 Score=42.60 Aligned_cols=35 Identities=31% Similarity=0.656 Sum_probs=30.1
Q ss_pred CCCCCcccCCCCCCCC-CHHHHHHHhhhhccCCCCc
Q 028603 41 DDVRPDFPCPYCYEDF-DIASLCSHLEDEHSCESKV 75 (206)
Q Consensus 41 dd~r~~F~CPfC~e~f-D~~~L~~H~~eeH~~e~k~ 75 (206)
++.+.-|.||+|.++| ++..|-+|.+.+|..+-..
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 4667899999999976 4788999999999998764
No 37
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=76.13 E-value=1.2 Score=33.70 Aligned_cols=27 Identities=30% Similarity=0.898 Sum_probs=18.4
Q ss_pred cccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCcccc
Q 028603 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
.|+||-||. -|+..+ +...-|||||-=
T Consensus 1 K~~CPCCg~~Tl~~~~-----------~~~ydIC~VC~W 28 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERG-----------EGTYDICPVCFW 28 (78)
T ss_pred CccCCCCCcEEeccCC-----------CcCceECCCCCc
Confidence 389999998 665432 223569999954
No 38
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.46 E-value=1.1 Score=40.64 Aligned_cols=13 Identities=31% Similarity=0.920 Sum_probs=9.6
Q ss_pred CcccCCCCCCCCC
Q 028603 45 PDFPCPYCYEDFD 57 (206)
Q Consensus 45 ~~F~CPfC~e~fD 57 (206)
.++.||+|+--|-
T Consensus 18 k~ieCPvC~tkFk 30 (267)
T COG1655 18 KTIECPVCNTKFK 30 (267)
T ss_pred ceeccCcccchhh
Confidence 3799999976443
No 39
>smart00355 ZnF_C2H2 zinc finger.
Probab=74.26 E-value=4.3 Score=21.86 Aligned_cols=23 Identities=26% Similarity=0.569 Sum_probs=16.2
Q ss_pred ccCCCCCC-CCCHHHHHHHhhhhcc
Q 028603 47 FPCPYCYE-DFDIASLCSHLEDEHS 70 (206)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~eeH~ 70 (206)
|.|+.|+. =-....|..|+. .|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHH-Hhc
Confidence 57888888 456667888876 443
No 40
>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=72.65 E-value=3.1 Score=29.90 Aligned_cols=37 Identities=19% Similarity=0.363 Sum_probs=24.3
Q ss_pred CCcccCCCCCC------------CCCHHHHHHHhhhhccCCCCceecCccccchh
Q 028603 44 RPDFPCPYCYE------------DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 44 r~~F~CPfC~e------------~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs 86 (206)
...|.||.|++ -||...+..++.. ...+||+|...++
T Consensus 2 P~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~ 50 (73)
T PF04564_consen 2 PDEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLS 50 (73)
T ss_dssp SGGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-S
T ss_pred CcccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCC
Confidence 34788888854 5778888777776 5679999977654
No 41
>PHA00616 hypothetical protein
Probab=72.32 E-value=2.5 Score=28.80 Aligned_cols=25 Identities=20% Similarity=0.267 Sum_probs=20.0
Q ss_pred ccCCCCCC-CCCHHHHHHHhhhhccC
Q 028603 47 FPCPYCYE-DFDIASLCSHLEDEHSC 71 (206)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~eeH~~ 71 (206)
|.||.||. =....+|..|+...|.-
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 78999998 56778888888877765
No 42
>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=72.20 E-value=1.3 Score=27.70 Aligned_cols=10 Identities=40% Similarity=1.062 Sum_probs=6.3
Q ss_pred CceecCcccc
Q 028603 74 KVTVCPICSV 83 (206)
Q Consensus 74 k~vVCPICa~ 83 (206)
..-+||+|.+
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 3457777755
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=71.86 E-value=1.6 Score=45.23 Aligned_cols=42 Identities=26% Similarity=0.517 Sum_probs=36.0
Q ss_pred CCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 44 RPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 44 r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.+..+||||+. .-.+..|.+|+.-.|---.-+.-|+.|....
T Consensus 208 sqlltcpycdrgykrltslkeHikyrhekne~nfsC~lCsytF 250 (1007)
T KOG3623|consen 208 SQLLTCPYCDRGYKRLTSLKEHIKYRHEKNEPNFSCMLCSYTF 250 (1007)
T ss_pred hhhhcchhHHHHHHHHHHHHHHHHHHHhhCCCCCcchhhhhhh
Confidence 45689999999 5567899999999999877788899998863
No 44
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=71.56 E-value=2 Score=28.38 Aligned_cols=28 Identities=18% Similarity=0.719 Sum_probs=16.1
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
+|.||-||..|+.... .....||.|...
T Consensus 3 ~y~C~~CG~~~~~~~~-----------~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEY-----------GTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCC-----------CCceECCCCCCe
Confidence 5777777775554211 115677777654
No 45
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=70.67 E-value=1.8 Score=32.52 Aligned_cols=34 Identities=21% Similarity=0.615 Sum_probs=14.1
Q ss_pred CCcccCCCCC-C-CCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 44 RPDFPCPYCY-E-DFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 44 r~~F~CPfC~-e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
...|.||||+ + -+.+ .-.-......+.|-+|-..
T Consensus 20 ~~~F~CPfC~~~~sV~v-------~idkk~~~~~~~C~~Cg~~ 55 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSV-------KIDKKEGIGILSCRVCGES 55 (81)
T ss_dssp SS----TTT--SS-EEE-------EEETTTTEEEEEESSS--E
T ss_pred CceEcCCcCCCCCeEEE-------EEEccCCEEEEEecCCCCe
Confidence 3589999999 4 2221 1122233445789999654
No 46
>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=70.57 E-value=3.1 Score=28.34 Aligned_cols=9 Identities=22% Similarity=0.490 Sum_probs=4.2
Q ss_pred CCHHHHHHH
Q 028603 56 FDIASLCSH 64 (206)
Q Consensus 56 fD~~~L~~H 64 (206)
+...+|..|
T Consensus 12 Y~~~~LlqH 20 (43)
T PF03470_consen 12 YKYRELLQH 20 (43)
T ss_pred eehhHHHHH
Confidence 444444444
No 47
>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=69.23 E-value=4.3 Score=27.54 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=20.3
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhcc
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHS 70 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~ 70 (206)
.+.||.|...+.. .|..|+...|.
T Consensus 31 ~v~CPiC~~~~~~-~l~~Hl~~~H~ 54 (54)
T PF05605_consen 31 NVVCPICSSRVTD-NLIRHLNSQHR 54 (54)
T ss_pred CccCCCchhhhhh-HHHHHHHHhcC
Confidence 6999999986654 99999998884
No 48
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=68.99 E-value=1.5 Score=34.05 Aligned_cols=33 Identities=18% Similarity=0.455 Sum_probs=21.4
Q ss_pred CCCCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 41 DDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 41 dd~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
....+.|.||||+. .+...+ ..--.|--|-..+
T Consensus 31 ~~q~a~y~CpfCgk~~vkR~a------------~GIW~C~~C~~~~ 64 (90)
T PTZ00255 31 ISQHAKYFCPFCGKHAVKRQA------------VGIWRCKGCKKTV 64 (90)
T ss_pred HHHhCCccCCCCCCCceeeee------------eEEEEcCCCCCEE
Confidence 46678999999997 554332 1224577776654
No 49
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=68.33 E-value=4 Score=29.54 Aligned_cols=34 Identities=29% Similarity=0.658 Sum_probs=24.4
Q ss_pred CCCCcccCCCCCCC-CCHHHHHHHhhhhccCCCCceecCccc
Q 028603 42 DVRPDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICS 82 (206)
Q Consensus 42 d~r~~F~CPfC~e~-fD~~~L~~H~~eeH~~e~k~vVCPICa 82 (206)
+-...|.||-||+. +-. |..|... .+.-+||-|-
T Consensus 21 ~~~~~F~CPnCG~~~I~R---C~~CRk~----~~~Y~CP~CG 55 (59)
T PRK14890 21 EKAVKFLCPNCGEVIIYR---CEKCRKQ----SNPYTCPKCG 55 (59)
T ss_pred CccCEeeCCCCCCeeEee---chhHHhc----CCceECCCCC
Confidence 33568999999994 555 5555554 5678999884
No 50
>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=68.19 E-value=2.3 Score=29.06 Aligned_cols=30 Identities=27% Similarity=0.652 Sum_probs=16.4
Q ss_pred cCCCCCC-CCCHHHHHHHhhhhcc-C-CCCceecCccccc
Q 028603 48 PCPYCYE-DFDIASLCSHLEDEHS-C-ESKVTVCPICSVK 84 (206)
Q Consensus 48 ~CPfC~e-~fD~~~L~~H~~eeH~-~-e~k~vVCPICa~~ 84 (206)
+|||||. +.-+. ..+. . ......|+-|-+.
T Consensus 3 PCPfCGg~~~~~~-------~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 3 PCPFCGGADVYLR-------RGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCcceeeE-------eccCCCCCEEEEECCCCCCC
Confidence 7999998 43221 1111 1 1223469999765
No 51
>PRK12495 hypothetical protein; Provisional
Probab=65.80 E-value=3.8 Score=36.65 Aligned_cols=29 Identities=21% Similarity=0.478 Sum_probs=22.4
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccchh
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs 86 (206)
..|.||.||..+- .. ...++||+|-..+.
T Consensus 41 sa~hC~~CG~PIp------------a~-pG~~~Cp~CQ~~~~ 69 (226)
T PRK12495 41 TNAHCDECGDPIF------------RH-DGQEFCPTCQQPVT 69 (226)
T ss_pred chhhcccccCccc------------CC-CCeeECCCCCCccc
Confidence 4699999999554 22 56689999998874
No 52
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.79 E-value=4.4 Score=34.35 Aligned_cols=34 Identities=24% Similarity=0.443 Sum_probs=24.9
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.....|.||-|+.-|+..+-.+ ..-.||+|-..+
T Consensus 113 ~~~~~Y~Cp~C~~rytf~eA~~----------~~F~Cp~Cg~~L 146 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTFDEAME----------YGFRCPQCGEML 146 (178)
T ss_pred cCCCEEECCCCCcEEeHHHHhh----------cCCcCCCCCCCC
Confidence 3457899999999666655432 256999998875
No 53
>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=65.73 E-value=3.6 Score=23.64 Aligned_cols=23 Identities=22% Similarity=0.398 Sum_probs=16.6
Q ss_pred ccCCCCCC-CCCHHHHHHHhhhhc
Q 028603 47 FPCPYCYE-DFDIASLCSHLEDEH 69 (206)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~eeH 69 (206)
|.|..|++ =-+...|..|.+..|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhc
Confidence 67888888 456777888875544
No 54
>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=65.60 E-value=2.1 Score=27.15 Aligned_cols=26 Identities=27% Similarity=0.599 Sum_probs=16.1
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
.|.|+.||.-++... ..-+||||-+.
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 467888887333211 23489999764
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=65.32 E-value=4.7 Score=33.37 Aligned_cols=34 Identities=21% Similarity=0.377 Sum_probs=26.2
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.....|.||-|+.-|+..+-.+ ..-.||+|-..+
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~----------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME----------LNFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH----------cCCcCCCCCCEe
Confidence 3456899999999777666654 256999998875
No 56
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=64.59 E-value=2.4 Score=28.55 Aligned_cols=45 Identities=36% Similarity=0.725 Sum_probs=28.8
Q ss_pred cccCCC--CCCCCCHHHHHHHhhhhccCCCCceecCc----cccchh-hhHhhh
Q 028603 46 DFPCPY--CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVKVA-RDMLSH 92 (206)
Q Consensus 46 ~F~CPf--C~e~fD~~~L~~H~~eeH~~e~k~vVCPI----Ca~~vs-~d~l~H 92 (206)
...||+ |.+.+-...|-.|+..+=+ .+.+.||. |..++. .+|..|
T Consensus 9 ~v~C~~~cc~~~i~r~~l~~H~~~~C~--~~~v~C~~~~~GC~~~~~~~~l~~H 60 (60)
T PF02176_consen 9 PVPCPNGCCNEMIPRKELDDHLENECP--KRPVPCPYSPYGCKERVPREDLEEH 60 (60)
T ss_dssp EEE-TT--S-BEEECCCHHHHHHTTST--TSEEE-SS----S--EEEHHHHHHC
T ss_pred EeeCCCCCcccceeHHHHHHHHHccCC--CCcEECCCCCCCCCCccchhHHhCC
Confidence 568999 6667888899999985432 35789999 988764 456554
No 57
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=63.94 E-value=5.1 Score=38.89 Aligned_cols=63 Identities=21% Similarity=0.426 Sum_probs=38.2
Q ss_pred CCCCCCCCCCCCcccCCCCCCC---CCHHHHHHHhhhhccCCCCceecCccccch-----------hhhHhhhhhccccc
Q 028603 34 IDDFEVEDDVRPDFPCPYCYED---FDIASLCSHLEDEHSCESKVTVCPICSVKV-----------ARDMLSHITLQHGH 99 (206)
Q Consensus 34 ~d~~e~ddd~r~~F~CPfC~e~---fD~~~L~~H~~eeH~~e~k~vVCPICa~~v-----------s~d~l~HL~~qH~~ 99 (206)
+++.+.++..++.|.||+|... ||...|..- +...-.|-.|-.-+ ++..+++++-|=..
T Consensus 116 led~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~-------~~~~F~C~~C~gelveDe~~~~~~e~~~~l~~~~~Q~~p 188 (436)
T KOG2593|consen 116 LEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDN-------ETGEFHCENCGGELVEDENKLPSKESRTALNRLMEQLEP 188 (436)
T ss_pred HHHHhhhccccccccCCccccchhhhHHHHhhcc-------cCceEEEecCCCchhcccccCchHHHHHHHHHHHHHHHH
Confidence 4444445566899999999984 555555432 23446788886543 33556666665555
Q ss_pred hhhh
Q 028603 100 LFKL 103 (206)
Q Consensus 100 ~~k~ 103 (206)
.++.
T Consensus 189 i~d~ 192 (436)
T KOG2593|consen 189 IIDL 192 (436)
T ss_pred HHHH
Confidence 5554
No 58
>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=62.59 E-value=2.1 Score=33.27 Aligned_cols=17 Identities=18% Similarity=0.704 Sum_probs=13.3
Q ss_pred CCCCCcccCCCCCC-CCC
Q 028603 41 DDVRPDFPCPYCYE-DFD 57 (206)
Q Consensus 41 dd~r~~F~CPfC~e-~fD 57 (206)
......|.||||+. .+-
T Consensus 30 ~~q~a~y~CpfCgk~~vk 47 (91)
T TIGR00280 30 IQQKAKYVCPFCGKKTVK 47 (91)
T ss_pred HHHhcCccCCCCCCCceE
Confidence 46678999999987 543
No 59
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=61.94 E-value=5.3 Score=38.32 Aligned_cols=35 Identities=31% Similarity=0.747 Sum_probs=20.4
Q ss_pred CCCCCCCCCHHH-----------HHHHhhhhccCCCCceecCccccc
Q 028603 49 CPYCYEDFDIAS-----------LCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 49 CPfC~e~fD~~~-----------L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
||.|-|.+|+.. +|..|- .|.-+.-++.||.|.-+
T Consensus 17 cplcie~mditdknf~pc~cgy~ic~fc~-~~irq~lngrcpacrr~ 62 (480)
T COG5175 17 CPLCIEPMDITDKNFFPCPCGYQICQFCY-NNIRQNLNGRCPACRRK 62 (480)
T ss_pred CcccccccccccCCcccCCcccHHHHHHH-HHHHhhccCCChHhhhh
Confidence 777766666532 333322 12223368999999876
No 60
>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=61.53 E-value=6.7 Score=38.33 Aligned_cols=42 Identities=31% Similarity=0.351 Sum_probs=33.1
Q ss_pred CCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCc---eecCccccc
Q 028603 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKV---TVCPICSVK 84 (206)
Q Consensus 43 ~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~---vVCPICa~~ 84 (206)
-+.--.||+|.+ -.|..++..|+..+|...-.+ -+.|-+...
T Consensus 54 sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~P~lqs~lPqrId~ 99 (466)
T PF04780_consen 54 SWRFWICPRCSKKFSDAESCLSHMEQEHPAGLKPKLQSVLPQRIDD 99 (466)
T ss_pred ceeEeeCCcccceeCCHHHHHHHHHHhhhhhcChhhhhhcCcccCH
Confidence 355678999999 999999999999999986543 356665553
No 61
>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=61.42 E-value=5.8 Score=27.44 Aligned_cols=14 Identities=36% Similarity=0.942 Sum_probs=11.5
Q ss_pred CCCCCcccCCCCCC
Q 028603 41 DDVRPDFPCPYCYE 54 (206)
Q Consensus 41 dd~r~~F~CPfC~e 54 (206)
+++..+|.||.|+.
T Consensus 29 ~~Lp~~w~CP~C~a 42 (50)
T cd00730 29 EDLPDDWVCPVCGA 42 (50)
T ss_pred hHCCCCCCCCCCCC
Confidence 35678999999987
No 62
>PF12773 DZR: Double zinc ribbon
Probab=61.11 E-value=4.2 Score=26.78 Aligned_cols=28 Identities=21% Similarity=0.562 Sum_probs=19.1
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccchh
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs 86 (206)
=.||.||..+. ..+...++||.|.+.+.
T Consensus 13 ~fC~~CG~~l~------------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 13 KFCPHCGTPLP------------PPDQSKKICPNCGAENP 40 (50)
T ss_pred cCChhhcCChh------------hccCCCCCCcCCcCCCc
Confidence 35788877665 44555678999987653
No 63
>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=60.53 E-value=4.2 Score=27.80 Aligned_cols=14 Identities=36% Similarity=0.942 Sum_probs=8.9
Q ss_pred CCCCCcccCCCCCC
Q 028603 41 DDVRPDFPCPYCYE 54 (206)
Q Consensus 41 dd~r~~F~CPfC~e 54 (206)
+++...|.||-|+.
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 36678999999986
No 64
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=60.07 E-value=2.6 Score=32.72 Aligned_cols=17 Identities=24% Similarity=0.694 Sum_probs=13.2
Q ss_pred CCCCCcccCCCCCC-CCC
Q 028603 41 DDVRPDFPCPYCYE-DFD 57 (206)
Q Consensus 41 dd~r~~F~CPfC~e-~fD 57 (206)
....+.|+||||+. .+-
T Consensus 31 ~~q~a~y~CpfCgk~~vk 48 (90)
T PRK03976 31 EKMRAKHVCPVCGRPKVK 48 (90)
T ss_pred HHHhcCccCCCCCCCceE
Confidence 46678999999987 543
No 65
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=59.34 E-value=8.4 Score=27.01 Aligned_cols=33 Identities=15% Similarity=0.425 Sum_probs=17.1
Q ss_pred CCCcccCCCCC-------------CCCCHHHHHHHhhhhccCCCCceecCc
Q 028603 43 VRPDFPCPYCY-------------EDFDIASLCSHLEDEHSCESKVTVCPI 80 (206)
Q Consensus 43 ~r~~F~CPfC~-------------e~fD~~~L~~H~~eeH~~e~k~vVCPI 80 (206)
....|.||+.. --|+...+..++ ...+.+.||+
T Consensus 8 ~~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv 53 (57)
T PF11789_consen 8 GTISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPV 53 (57)
T ss_dssp SB--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHC-----TTTS-EE-SC
T ss_pred cEeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCC
Confidence 34456777653 346666666666 3456688998
No 66
>PF13395 HNH_4: HNH endonuclease
Probab=59.00 E-value=5.2 Score=27.29 Aligned_cols=14 Identities=43% Similarity=1.058 Sum_probs=12.1
Q ss_pred CCCCCCCCCHHHHH
Q 028603 49 CPYCYEDFDIASLC 62 (206)
Q Consensus 49 CPfC~e~fD~~~L~ 62 (206)
|||||+.++...|.
T Consensus 1 C~Y~g~~i~~~~l~ 14 (54)
T PF13395_consen 1 CPYCGKPISIENLF 14 (54)
T ss_pred CCCCCCCCChhhcc
Confidence 99999999988764
No 67
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=58.89 E-value=4.3 Score=32.39 Aligned_cols=36 Identities=19% Similarity=0.452 Sum_probs=21.1
Q ss_pred CCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 44 r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
.-+|+||||+..--.+-+ -.-......++|-+|-..
T Consensus 20 ~k~FtCp~Cghe~vs~ct-----vkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCT-----VKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred CceEecCccCCeeeeEEE-----EEecCceeEEEcccCcce
Confidence 458999999983322211 111122345789999654
No 68
>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=58.17 E-value=5.5 Score=23.98 Aligned_cols=12 Identities=42% Similarity=0.869 Sum_probs=9.8
Q ss_pred CCCcccCCCCCC
Q 028603 43 VRPDFPCPYCYE 54 (206)
Q Consensus 43 ~r~~F~CPfC~e 54 (206)
....|.||-||+
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 356899999996
No 69
>PRK00420 hypothetical protein; Validated
Probab=58.07 E-value=7.7 Score=31.10 Aligned_cols=27 Identities=22% Similarity=0.369 Sum_probs=18.8
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
-.||.||..|-. .....++||+|...+
T Consensus 24 ~~CP~Cg~pLf~------------lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFE------------LKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCccee------------cCCCceECCCCCCee
Confidence 589999974321 124568999998864
No 70
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=57.19 E-value=5.4 Score=26.82 Aligned_cols=28 Identities=21% Similarity=0.553 Sum_probs=21.2
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.|.|.-||.++++. ....+.||-|..++
T Consensus 2 ~Y~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC------------CCCceECCCCCceE
Confidence 58899999977754 34568999997664
No 71
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=54.58 E-value=5.8 Score=37.54 Aligned_cols=58 Identities=29% Similarity=0.559 Sum_probs=37.3
Q ss_pred cccCCCCCCCCCHHH---HHHHhhhhccCCCC-ceecCccccch--------------------------hhhHhhhhhc
Q 028603 46 DFPCPYCYEDFDIAS---LCSHLEDEHSCESK-VTVCPICSVKV--------------------------ARDMLSHITL 95 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~---L~~H~~eeH~~e~k-~vVCPICa~~v--------------------------s~d~l~HL~~ 95 (206)
.-.|--|+.-+-+-+ =|+|+-=.-|.-.. -.+||.|..+| -+||..||++
T Consensus 90 VHfCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~VqrIeq~~~g~iFmC~~~~GC~RTyLsqrDlqAHInh 169 (389)
T KOG2932|consen 90 VHFCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQRIEQIMMGGIFMCAAPHGCLRTYLSQRDLQAHINH 169 (389)
T ss_pred eEeecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHHHHHhcccceEEeecchhHHHHHhhHHHHHHHhhh
Confidence 455666766444433 25554433333222 35899999875 3699999999
Q ss_pred cccchhhh
Q 028603 96 QHGHLFKL 103 (206)
Q Consensus 96 qH~~~~k~ 103 (206)
+|+...+-
T Consensus 170 rH~~~~~p 177 (389)
T KOG2932|consen 170 RHGSLLQP 177 (389)
T ss_pred hhccccCC
Confidence 99977654
No 72
>PF15616 TerY-C: TerY-C metal binding domain
Probab=54.48 E-value=3.3 Score=34.02 Aligned_cols=44 Identities=16% Similarity=0.257 Sum_probs=31.3
Q ss_pred CCcccCCCCCCCCCHHHHHHHhhhhccC-CCCceecCccccchhhhH
Q 028603 44 RPDFPCPYCYEDFDIASLCSHLEDEHSC-ESKVTVCPICSVKVARDM 89 (206)
Q Consensus 44 r~~F~CPfC~e~fD~~~L~~H~~eeH~~-e~k~vVCPICa~~vs~d~ 89 (206)
.-.-.||+||..+-++-. =|-.-|+. +...++||-|-....-..
T Consensus 75 ~g~PgCP~CGn~~~fa~C--~CGkl~Ci~g~~~~~CPwCg~~g~~~~ 119 (131)
T PF15616_consen 75 IGAPGCPHCGNQYAFAVC--GCGKLFCIDGEGEVTCPWCGNEGSFGA 119 (131)
T ss_pred cCCCCCCCCcChhcEEEe--cCCCEEEeCCCCCEECCCCCCeeeecc
Confidence 345789999995544432 58888985 556799999988764433
No 73
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=53.41 E-value=6 Score=31.23 Aligned_cols=9 Identities=67% Similarity=1.575 Sum_probs=7.5
Q ss_pred cccCCCCCC
Q 028603 46 DFPCPYCYE 54 (206)
Q Consensus 46 ~F~CPfC~e 54 (206)
-++|||||+
T Consensus 3 LI~CP~Cg~ 11 (97)
T COG4311 3 LIPCPYCGE 11 (97)
T ss_pred eecCCCCCC
Confidence 468999998
No 74
>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=53.18 E-value=3.1 Score=27.27 Aligned_cols=31 Identities=23% Similarity=0.635 Sum_probs=20.5
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCcccc
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
.+|.|+=||..|++..- ..+...+.||.|..
T Consensus 4 Yey~C~~Cg~~fe~~~~--------~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQS--------ISEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEE--------cCCCCCCcCCCCCC
Confidence 36889999876654321 12245688999976
No 75
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.82 E-value=12 Score=32.59 Aligned_cols=43 Identities=21% Similarity=0.589 Sum_probs=27.1
Q ss_pred CcccCCCCCCCCCHHH----HHHHhhhhccC---CCCceecCccccchhh
Q 028603 45 PDFPCPYCYEDFDIAS----LCSHLEDEHSC---ESKVTVCPICSVKVAR 87 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~----L~~H~~eeH~~---e~k~vVCPICa~~vs~ 87 (206)
..|.||.|-+.+.... =|-|+-=.-+. -.+.++||+|..+++.
T Consensus 130 ~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 130 GTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred cccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 5699999977555444 34444333332 1244799999988754
No 76
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.67 E-value=11 Score=32.12 Aligned_cols=45 Identities=20% Similarity=0.350 Sum_probs=29.7
Q ss_pred CCCCCCCCCCCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccchhhhHhhhh
Q 028603 33 SIDDFEVEDDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (206)
Q Consensus 33 ~~d~~e~ddd~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~d~l~HL 93 (206)
|+..+..+++....=.||.||. ...+...||.|-...-+|..+=+
T Consensus 296 ~~~~v~~~~~~~tS~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~ 340 (364)
T COG0675 296 GGIVVKVVPPYYTSKTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAAL 340 (364)
T ss_pred CCeEEEECCCCCCcccccccCC----------------ccceeEECCCCCCeehhhHHHHH
Confidence 3333333444455678999998 33667899999988766665433
No 77
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=52.54 E-value=13 Score=27.13 Aligned_cols=35 Identities=29% Similarity=0.722 Sum_probs=22.3
Q ss_pred CCCCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccc
Q 028603 41 DDVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICS 82 (206)
Q Consensus 41 dd~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa 82 (206)
+|....|+||-||+ .+-.-.-|.- -.+.-+||-|-
T Consensus 22 ~e~~v~F~CPnCGe~~I~Rc~~CRk-------~g~~Y~Cp~CG 57 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYRCAKCRK-------LGNPYRCPKCG 57 (61)
T ss_pred CCceeEeeCCCCCceeeehhhhHHH-------cCCceECCCcC
Confidence 35567899999997 6554433321 14456888884
No 78
>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=52.10 E-value=8.6 Score=23.25 Aligned_cols=8 Identities=38% Similarity=1.111 Sum_probs=3.9
Q ss_pred CCCCCCCC
Q 028603 49 CPYCYEDF 56 (206)
Q Consensus 49 CPfC~e~f 56 (206)
||-|+..+
T Consensus 3 CP~C~~~V 10 (26)
T PF10571_consen 3 CPECGAEV 10 (26)
T ss_pred CCCCcCCc
Confidence 55555443
No 79
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=50.44 E-value=12 Score=26.62 Aligned_cols=27 Identities=30% Similarity=0.778 Sum_probs=18.5
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.-.||.|++.|.. +.-.||||.|-+..
T Consensus 5 ~~~C~~Cg~~~~~-------------~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKD-------------GDDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccC-------------CCCEEECCCCCCcc
Confidence 3579999886631 23358999998753
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=49.89 E-value=19 Score=25.05 Aligned_cols=38 Identities=24% Similarity=0.577 Sum_probs=27.8
Q ss_pred CCCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccchhhhHhh
Q 028603 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLS 91 (206)
Q Consensus 42 d~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~d~l~ 91 (206)
+.-.+=.||.||. .-+ ....+..+||.|-....+|+.+
T Consensus 24 ~~~TSq~C~~CG~~~~~------------~~~~r~~~C~~Cg~~~~rD~na 62 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK------------RRSGRVFTCPNCGFEMDRDVNA 62 (69)
T ss_pred CCCCccCccCccccccc------------ccccceEEcCCCCCEECcHHHH
Confidence 4446778999998 333 4556678999998887776655
No 81
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=48.96 E-value=14 Score=23.93 Aligned_cols=20 Identities=30% Similarity=0.753 Sum_probs=11.6
Q ss_pred HHHHhhhhccCCCCceecCccc
Q 028603 61 LCSHLEDEHSCESKVTVCPICS 82 (206)
Q Consensus 61 L~~H~~eeH~~e~k~vVCPICa 82 (206)
+|.-|..... .+.++||+|.
T Consensus 24 ~C~~C~~~~~--~~~~~CP~C~ 43 (44)
T PF14634_consen 24 FCEKCLKKLK--GKSVKCPICR 43 (44)
T ss_pred HHHHHHHhhc--CCCCCCcCCC
Confidence 3444444433 5568888885
No 82
>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=48.29 E-value=7.1 Score=30.33 Aligned_cols=14 Identities=21% Similarity=0.826 Sum_probs=10.6
Q ss_pred CCCCCcccCCCCCC
Q 028603 41 DDVRPDFPCPYCYE 54 (206)
Q Consensus 41 dd~r~~F~CPfC~e 54 (206)
......|.|||||.
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 34567899999998
No 83
>PRK03922 hypothetical protein; Provisional
Probab=48.06 E-value=8.9 Score=31.00 Aligned_cols=13 Identities=46% Similarity=0.731 Sum_probs=11.0
Q ss_pred cccCCCCCCCCCH
Q 028603 46 DFPCPYCYEDFDI 58 (206)
Q Consensus 46 ~F~CPfC~e~fD~ 58 (206)
.-.||+||++|+-
T Consensus 49 ~~~cP~cge~~~~ 61 (113)
T PRK03922 49 LTICPKCGEPFDS 61 (113)
T ss_pred cccCCCCCCcCCc
Confidence 5689999999874
No 84
>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=47.90 E-value=4.9 Score=31.63 Aligned_cols=30 Identities=23% Similarity=0.430 Sum_probs=22.4
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
+.+..+.|+-|+..|..... ...||-|-..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-------------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEID-------------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCc-------------CccCcCCcCC
Confidence 45678999999987766533 3679999764
No 85
>PF14616 DUF4451: Domain of unknown function (DUF4451)
Probab=47.85 E-value=12 Score=30.11 Aligned_cols=28 Identities=21% Similarity=0.428 Sum_probs=22.4
Q ss_pred ceecCccccch-----hhhHhhhhhccccchhh
Q 028603 75 VTVCPICSVKV-----ARDMLSHITLQHGHLFK 102 (206)
Q Consensus 75 ~vVCPICa~~v-----s~d~l~HL~~qH~~~~k 102 (206)
.+.||+|.... ...+..||+..||-+-+
T Consensus 25 eGlCp~C~~~~wl~lKnSsY~~Hl~~~HGI~s~ 57 (124)
T PF14616_consen 25 EGLCPYCPGGNWLKLKNSSYWYHLQFAHGISST 57 (124)
T ss_pred eeECCCCCCCcEeeecccchhhhhhhccccccC
Confidence 78999998542 55799999999998653
No 86
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=47.25 E-value=9.3 Score=30.40 Aligned_cols=13 Identities=46% Similarity=0.912 Sum_probs=10.9
Q ss_pred cccCCCCCCCCCH
Q 028603 46 DFPCPYCYEDFDI 58 (206)
Q Consensus 46 ~F~CPfC~e~fD~ 58 (206)
.-.||+||++|+-
T Consensus 47 ~~~cP~Cge~~~~ 59 (102)
T PF04475_consen 47 DTICPKCGEELDS 59 (102)
T ss_pred cccCCCCCCccCc
Confidence 5689999998874
No 87
>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=47.13 E-value=9 Score=32.08 Aligned_cols=54 Identities=26% Similarity=0.566 Sum_probs=31.4
Q ss_pred CcccCCC----CCCCCCHHHHHHHhhhhccCCCCceecCc----cccc-hhhhHhhhhhccccchh
Q 028603 45 PDFPCPY----CYEDFDIASLCSHLEDEHSCESKVTVCPI----CSVK-VARDMLSHITLQHGHLF 101 (206)
Q Consensus 45 ~~F~CPf----C~e~fD~~~L~~H~~eeH~~e~k~vVCPI----Ca~~-vs~d~l~HL~~qH~~~~ 101 (206)
-.|+|+| |.+.+-......|.++ - .-+...||+ |.-. ...++..|+...|+...
T Consensus 13 ~~~pC~~~~~GC~~~~~~~~~~~HE~~-C--~~~p~~CP~~~~~C~~~G~~~~l~~Hl~~~H~~~~ 75 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPYSEKREHEEE-C--PFRPCSCPFPGSGCDWQGSYKELLDHLRDKHSWNV 75 (198)
T ss_dssp --EE-CCGGGT---EE-GGGHHHHHHT----TTSEEE-SSSSTT---EEECCCHHHHHHHHTTTSE
T ss_pred ceecCCCCCCCCcccccccChhhHhcc-C--CCcCCcCCCCCCCccccCCHHHHHHHHHHHCCCcc
Confidence 3799999 9888777777777633 1 234578999 6433 45689999999998743
No 88
>PRK12496 hypothetical protein; Provisional
Probab=45.63 E-value=14 Score=30.80 Aligned_cols=28 Identities=25% Similarity=0.481 Sum_probs=20.0
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccchh
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs 86 (206)
.|.|+-|+..|+.. ...-+||||-..+.
T Consensus 127 ~~~C~gC~~~~~~~-------------~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPED-------------YPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCC-------------CCCCcCCCCCChhh
Confidence 48899999877531 12248999987654
No 89
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.49 E-value=13 Score=21.98 Aligned_cols=9 Identities=33% Similarity=0.929 Sum_probs=5.6
Q ss_pred cCCCCCCCC
Q 028603 48 PCPYCYEDF 56 (206)
Q Consensus 48 ~CPfC~e~f 56 (206)
.||.||..+
T Consensus 4 ~Cp~Cg~~~ 12 (26)
T PF13248_consen 4 FCPNCGAEI 12 (26)
T ss_pred CCcccCCcC
Confidence 577777643
No 90
>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=45.25 E-value=14 Score=32.18 Aligned_cols=36 Identities=31% Similarity=0.572 Sum_probs=22.7
Q ss_pred CCCCCC--CCCHHHHHHHhhhhccC------CCCceecCccccc
Q 028603 49 CPYCYE--DFDIASLCSHLEDEHSC------ESKVTVCPICSVK 84 (206)
Q Consensus 49 CPfC~e--~fD~~~L~~H~~eeH~~------e~k~vVCPICa~~ 84 (206)
||.||. +-...+||.=|--+... .....+||.|-+.
T Consensus 1 C~~CG~~~~~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~ 44 (236)
T PF04981_consen 1 CPRCGREIEPLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRY 44 (236)
T ss_pred CCCCCCCCCCcccccChHHhcccCCeeecCCccCceECCCCCCE
Confidence 788887 33345777776655442 2245789999764
No 91
>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=45.13 E-value=14 Score=34.41 Aligned_cols=39 Identities=26% Similarity=0.500 Sum_probs=25.0
Q ss_pred cccCCCCCC--CCCHH----------HHHHHhhhhccCCCCceecCccccch
Q 028603 46 DFPCPYCYE--DFDIA----------SLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 46 ~F~CPfC~e--~fD~~----------~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.+.||.|.. .+.-. .+|..|.+..-.. ....||+|-..+
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~-~~~~CP~C~~~l 53 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR-GSGSCPECDTPL 53 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC-CCCCCCCCCCcc
Confidence 378999976 22211 3567777776433 446999997653
No 92
>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=44.84 E-value=21 Score=20.92 Aligned_cols=22 Identities=36% Similarity=0.715 Sum_probs=16.5
Q ss_pred HHHHHhhhhccCCCCceecCcccc
Q 028603 60 SLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 60 ~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
.|..|+.. |..+ +.-.||+|..
T Consensus 1 ~l~~H~~~-H~~~-k~~~C~~C~k 22 (26)
T PF13465_consen 1 NLRRHMRT-HTGE-KPYKCPYCGK 22 (26)
T ss_dssp HHHHHHHH-HSSS-SSEEESSSSE
T ss_pred CHHHHhhh-cCCC-CCCCCCCCcC
Confidence 37788884 7766 5689999964
No 93
>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=43.72 E-value=10 Score=26.53 Aligned_cols=9 Identities=44% Similarity=1.460 Sum_probs=8.3
Q ss_pred cccCCCCCC
Q 028603 46 DFPCPYCYE 54 (206)
Q Consensus 46 ~F~CPfC~e 54 (206)
.|.||+|+.
T Consensus 44 ~y~C~~Cg~ 52 (54)
T PF10058_consen 44 QYRCPYCGA 52 (54)
T ss_pred EEEcCCCCC
Confidence 899999986
No 94
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=42.66 E-value=13 Score=31.71 Aligned_cols=25 Identities=36% Similarity=0.805 Sum_probs=17.8
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
.+.||.||- + |.. -.+.+||||-+.
T Consensus 134 ~~vC~vCGy----------~---~~g-e~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGY----------T---HEG-EAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCC----------c---ccC-CCCCcCCCCCCh
Confidence 899999974 1 122 345799999764
No 95
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=42.62 E-value=29 Score=33.65 Aligned_cols=48 Identities=27% Similarity=0.538 Sum_probs=34.9
Q ss_pred cccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccch--hhhHhhhhh
Q 028603 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV--ARDMLSHIT 94 (206)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v--s~d~l~HL~ 94 (206)
.|+||.|+- ==-.++|..|+.-.|.- .+.-.|--|...- -.|+..|+.
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 688888888 33467888888888876 6777888887763 345666655
No 96
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=42.59 E-value=20 Score=21.48 Aligned_cols=22 Identities=32% Similarity=0.606 Sum_probs=15.4
Q ss_pred cccCCCCCCCCC-HHHHHHHhhh
Q 028603 46 DFPCPYCYEDFD-IASLCSHLED 67 (206)
Q Consensus 46 ~F~CPfC~e~fD-~~~L~~H~~e 67 (206)
.|.|.+|+..|. ...+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 477888888555 6777777654
No 97
>PRK11595 DNA utilization protein GntX; Provisional
Probab=42.56 E-value=12 Score=32.11 Aligned_cols=34 Identities=24% Similarity=0.459 Sum_probs=18.6
Q ss_pred cCCCCCCCCC--HHHHHHHhhhhccCCCCceecCcccc
Q 028603 48 PCPYCYEDFD--IASLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 48 ~CPfC~e~fD--~~~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
.|++|++.+. ...||..|.+.=..- ...||.|..
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~--~~~C~~Cg~ 42 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTL--KTCCPQCGL 42 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcc--cCcCccCCC
Confidence 4888877443 235777776553221 235655543
No 98
>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=42.55 E-value=3.1 Score=35.15 Aligned_cols=40 Identities=25% Similarity=0.613 Sum_probs=19.7
Q ss_pred CCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 44 r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
+-.|.||.|+..+...++.. .+.-........||-|....
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~--~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFE--EDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS----SSEEEETTEEEETTT--B-
T ss_pred ceEeECCCCCCCcccccccc--CCccccccCcCcCCCCCCcC
Confidence 34799999999776666543 11112234457899998864
No 99
>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=42.49 E-value=15 Score=29.11 Aligned_cols=33 Identities=24% Similarity=0.666 Sum_probs=23.4
Q ss_pred CCCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccchhh
Q 028603 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (206)
Q Consensus 42 d~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~ 87 (206)
|+-....||-||. =||+ ...++|||-|.+....
T Consensus 5 elGtKR~Cp~CG~kFYDL-------------nk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDL-------------NKDPIVCPKCGTEFPP 38 (108)
T ss_pred ccCCcccCCCCcchhccC-------------CCCCccCCCCCCccCc
Confidence 4556789999998 4443 2356899999887543
No 100
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=42.14 E-value=4.4 Score=32.56 Aligned_cols=40 Identities=23% Similarity=0.674 Sum_probs=26.1
Q ss_pred CCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch---------------hhhHhhhhhccccchhhh
Q 028603 49 CPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV---------------ARDMLSHITLQHGHLFKL 103 (206)
Q Consensus 49 CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v---------------s~d~l~HL~~qH~~~~k~ 103 (206)
||.||..+-+..| .||-|...| -.+|+.=+....|+.-++
T Consensus 1 CPvCg~~l~vt~l---------------~C~~C~t~i~G~F~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~ 55 (113)
T PF09862_consen 1 CPVCGGELVVTRL---------------KCPSCGTEIEGEFELPWFARLSPEQLEFIKLFIKNRGNLKEM 55 (113)
T ss_pred CCCCCCceEEEEE---------------EcCCCCCEEEeeeccchhhcCCHHHHHHHHHHHHhcCCHHHH
Confidence 8999987766544 677776654 236776666666665444
No 101
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=41.51 E-value=12 Score=30.19 Aligned_cols=26 Identities=27% Similarity=0.861 Sum_probs=15.7
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
-+||-|+.++.- .+....|||-|+.-
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 367777654431 13445788888764
No 102
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=41.11 E-value=5.8 Score=34.48 Aligned_cols=26 Identities=19% Similarity=0.598 Sum_probs=17.7
Q ss_pred cccCCCCCCCCCH--HHHHHHhhhhccCCC
Q 028603 46 DFPCPYCYEDFDI--ASLCSHLEDEHSCES 73 (206)
Q Consensus 46 ~F~CPfC~e~fD~--~~L~~H~~eeH~~e~ 73 (206)
.|.||.|+..+.+ .+| +|...|.++.
T Consensus 2 ~~~CP~C~~~l~~~~~~~--~C~~~h~fd~ 29 (272)
T PRK11088 2 SYQCPLCHQPLTLEENSW--ICPQNHQFDC 29 (272)
T ss_pred cccCCCCCcchhcCCCEE--EcCCCCCCcc
Confidence 4899999996643 333 5666777743
No 103
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=41.05 E-value=25 Score=22.43 Aligned_cols=31 Identities=23% Similarity=0.651 Sum_probs=18.1
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCcccc
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
..||-|+..|.+..= .=+...+.|.||-|..
T Consensus 3 i~CP~C~~~f~v~~~------~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDD------KLPAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCHH------HcccCCcEEECCCCCc
Confidence 468888885444321 0123355688888864
No 104
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.70 E-value=11 Score=30.41 Aligned_cols=36 Identities=25% Similarity=0.626 Sum_probs=22.6
Q ss_pred CcccCCCCCCCCCHH-H------HHHHhhhhccCCCCceecCccc
Q 028603 45 PDFPCPYCYEDFDIA-S------LCSHLEDEHSCESKVTVCPICS 82 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~-~------L~~H~~eeH~~e~k~vVCPICa 82 (206)
..+.||.|.+.|... . +|.-|...... ....||+|.
T Consensus 12 ~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~--~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREPVLLPCGHNFCRACLTRSWE--GPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcCccccccchHhHHHHHHhcC--CCcCCcccC
Confidence 478999998866555 2 23333333333 448999999
No 105
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=40.69 E-value=19 Score=32.69 Aligned_cols=40 Identities=20% Similarity=0.509 Sum_probs=28.4
Q ss_pred CCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccchhhhHhhhh
Q 028603 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHI 93 (206)
Q Consensus 43 ~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~d~l~HL 93 (206)
......||.||. ++ +.+ .+...+||.-|-..+..+++.+-
T Consensus 8 ~~~~~~Cp~Cg~~~i--------v~d---~~~Ge~vC~~CG~Vl~e~~iD~g 48 (310)
T PRK00423 8 EEEKLVCPECGSDKL--------IYD---YERGEIVCADCGLVIEENIIDQG 48 (310)
T ss_pred cccCCcCcCCCCCCe--------eEE---CCCCeEeecccCCcccccccccC
Confidence 334568999996 22 122 35778999999999988887643
No 106
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=40.45 E-value=21 Score=22.84 Aligned_cols=24 Identities=21% Similarity=0.551 Sum_probs=10.7
Q ss_pred CceecCccccch------hhhHhhhhhccc
Q 028603 74 KVTVCPICSVKV------ARDMLSHITLQH 97 (206)
Q Consensus 74 k~vVCPICa~~v------s~d~l~HL~~qH 97 (206)
..+.|-.|-..+ +.+|..||...|
T Consensus 15 ~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 15 KKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp S-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 345555554443 235555554443
No 107
>smart00507 HNHc HNH nucleases.
Probab=39.97 E-value=4.4 Score=25.28 Aligned_cols=21 Identities=19% Similarity=0.281 Sum_probs=13.2
Q ss_pred ccCCCCCCCCCHHHHHHHhhh
Q 028603 47 FPCPYCYEDFDIASLCSHLED 67 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~e 67 (206)
+.|+||+..++..--+.|+..
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 789999996553223445543
No 108
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=39.75 E-value=15 Score=26.15 Aligned_cols=22 Identities=32% Similarity=0.609 Sum_probs=14.6
Q ss_pred CCCcccCCCCCCCCCHHHHHHHhhhhccC
Q 028603 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSC 71 (206)
Q Consensus 43 ~r~~F~CPfC~e~fD~~~L~~H~~eeH~~ 71 (206)
.+..|.||.||-- -||-.+|-.
T Consensus 11 ~~v~~~Cp~cGip-------thcS~ehw~ 32 (55)
T PF13824_consen 11 AHVNFECPDCGIP-------THCSEEHWE 32 (55)
T ss_pred cccCCcCCCCCCc-------CccCHHHHH
Confidence 3568999999863 255555543
No 109
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=39.40 E-value=9 Score=30.10 Aligned_cols=30 Identities=20% Similarity=0.331 Sum_probs=21.3
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
+.+..+.|+-||..|.+.. ....||-|-..
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~ 95 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ-------------HDAQCPHCHGE 95 (113)
T ss_pred eeCcEEEcccCCCEEecCC-------------cCccCcCCCCC
Confidence 4567899999998665543 23469999753
No 110
>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=39.16 E-value=11 Score=30.85 Aligned_cols=40 Identities=20% Similarity=0.630 Sum_probs=29.3
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccchhhhHh
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDML 90 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~d~l 90 (206)
.+.|.-|+..++...+......... ..||.|...+..|++
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~~~-----~~C~~C~~~lrp~vv 144 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEEEP-----PRCPKCGGLLRPDVV 144 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTTSS-----CBCTTTSCBEEEEE-
T ss_pred eeeecCCCccccchhhccccccccc-----ccccccCccCCCCee
Confidence 5899999998888777665554432 399999997665554
No 111
>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=37.06 E-value=21 Score=20.74 Aligned_cols=20 Identities=25% Similarity=0.404 Sum_probs=12.6
Q ss_pred ccCCCCCC-CCCHHHHHHHhh
Q 028603 47 FPCPYCYE-DFDIASLCSHLE 66 (206)
Q Consensus 47 F~CPfC~e-~fD~~~L~~H~~ 66 (206)
|.|+.|+. =-+...|..|+.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCcccCCCCcCCHHHHHHHHc
Confidence 66777777 445666666654
No 112
>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=37.04 E-value=14 Score=25.07 Aligned_cols=14 Identities=29% Similarity=0.591 Sum_probs=7.7
Q ss_pred cCCCCCCCCCHHHH
Q 028603 48 PCPYCYEDFDIASL 61 (206)
Q Consensus 48 ~CPfC~e~fD~~~L 61 (206)
.||.|+.+||...-
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999998886544
No 113
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=36.88 E-value=11 Score=29.35 Aligned_cols=16 Identities=13% Similarity=0.673 Sum_probs=12.5
Q ss_pred CCCCcccCCCCCC-CCC
Q 028603 42 DVRPDFPCPYCYE-DFD 57 (206)
Q Consensus 42 d~r~~F~CPfC~e-~fD 57 (206)
...+.|.|+|||+ .+-
T Consensus 32 ~Qhaky~CsfCGK~~vK 48 (92)
T KOG0402|consen 32 QQHAKYTCSFCGKKTVK 48 (92)
T ss_pred HHhhhhhhhhcchhhhh
Confidence 4567899999998 443
No 114
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=36.85 E-value=7.5 Score=30.26 Aligned_cols=33 Identities=24% Similarity=0.604 Sum_probs=21.3
Q ss_pred CCCCCCcccCCCCCCC-CCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 40 EDDVRPDFPCPYCYED-FDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 40 ddd~r~~F~CPfC~e~-fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
|..+++.+.||+|+.. +. +....--.|.-|-..
T Consensus 29 e~~~~~~~~Cp~C~~~~Vk------------R~a~GIW~C~kCg~~ 62 (89)
T COG1997 29 EAQQRAKHVCPFCGRTTVK------------RIATGIWKCRKCGAK 62 (89)
T ss_pred HHHHhcCCcCCCCCCccee------------eeccCeEEcCCCCCe
Confidence 4567889999999873 22 122334567777654
No 115
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=36.84 E-value=18 Score=34.12 Aligned_cols=40 Identities=30% Similarity=0.547 Sum_probs=29.3
Q ss_pred CCcccCCCCCCCCC--HHHHHHHhhhh-ccC-----CCCceecCcccc
Q 028603 44 RPDFPCPYCYEDFD--IASLCSHLEDE-HSC-----ESKVTVCPICSV 83 (206)
Q Consensus 44 r~~F~CPfC~e~fD--~~~L~~H~~ee-H~~-----e~k~vVCPICa~ 83 (206)
..+-.||.||...| +.+||.=|--+ |.. +.+..+|+.|-+
T Consensus 4 ~~~~~C~~CGr~~~~~~~~lC~dC~~~~~~~~~ip~~~~v~~C~~Cga 51 (355)
T COG1499 4 ASTILCVRCGRSVDPLIDGLCGDCYVETTPLIEIPDEVNVEVCRHCGA 51 (355)
T ss_pred CcccEeccCCCcCchhhccccHHHHhccCccccCCCceEEEECCcCCC
Confidence 34678999999887 88888888766 544 333478999864
No 116
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.63 E-value=10 Score=30.66 Aligned_cols=18 Identities=11% Similarity=0.497 Sum_probs=13.6
Q ss_pred CCCCcccCCCCCCCCCHH
Q 028603 42 DVRPDFPCPYCYEDFDIA 59 (206)
Q Consensus 42 d~r~~F~CPfC~e~fD~~ 59 (206)
..+..+.|+-||..+...
T Consensus 66 ~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred ecceEEECCCCCCEEecc
Confidence 456789999999865544
No 117
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=36.29 E-value=19 Score=23.97 Aligned_cols=26 Identities=27% Similarity=0.589 Sum_probs=15.6
Q ss_pred CcccCCCCCCCCCHH------HHHHHhhhhcc
Q 028603 45 PDFPCPYCYEDFDIA------SLCSHLEDEHS 70 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~------~L~~H~~eeH~ 70 (206)
+.-.|-+|+..+... .|..|+...|+
T Consensus 17 ~~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 17 QRAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred eEEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 556677777755443 56666665554
No 118
>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=36.11 E-value=25 Score=24.91 Aligned_cols=38 Identities=24% Similarity=0.482 Sum_probs=23.8
Q ss_pred cccCCCCCCCCCHHHHHHHhh-----------------hhccCCCCceecCcccc
Q 028603 46 DFPCPYCYEDFDIASLCSHLE-----------------DEHSCESKVTVCPICSV 83 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~-----------------eeH~~e~k~vVCPICa~ 83 (206)
...||+|.-.+|-..|+.=.. -+........+||.|..
T Consensus 7 iL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r 61 (68)
T PF03966_consen 7 ILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVEGELICPECGR 61 (68)
T ss_dssp TBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTE
T ss_pred hhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccCCEEEcCCCCC
Confidence 568999988887777766221 12233335689999954
No 119
>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=35.97 E-value=13 Score=35.91 Aligned_cols=34 Identities=35% Similarity=0.926 Sum_probs=15.5
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCcc-ccchhhhHhh
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPIC-SVKVARDMLS 91 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPIC-a~~vs~d~l~ 91 (206)
+.-.|||||.-| |+ +-+--+|||| .+.||.+-+|
T Consensus 379 ~~v~CP~cgA~y------------~~-~~kG~lC~vC~l~~IG~~a~G 413 (422)
T PF06957_consen 379 PSVKCPYCGAKY------------HP-EYKGQLCPVCELSEIGADASG 413 (422)
T ss_dssp -EEE-TTT--EE------------EG-GGTTSB-TTTTTBBTT---S-
T ss_pred CCeeCCCCCCcc------------Ch-hhCCCCCCCCcceeeCCccee
Confidence 456799998743 21 2234699999 4567765543
No 120
>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=35.89 E-value=16 Score=22.68 Aligned_cols=9 Identities=44% Similarity=1.176 Sum_probs=4.7
Q ss_pred CCceecCcc
Q 028603 73 SKVTVCPIC 81 (206)
Q Consensus 73 ~k~vVCPIC 81 (206)
...+.||+|
T Consensus 33 ~~~~~CP~C 41 (41)
T PF00097_consen 33 SGSVKCPLC 41 (41)
T ss_dssp TSSSBTTTT
T ss_pred cCCccCCcC
Confidence 344456665
No 121
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.79 E-value=10 Score=35.15 Aligned_cols=41 Identities=27% Similarity=0.536 Sum_probs=26.6
Q ss_pred CcccCCCCCC--CCCHHHH-HHHhhhhccCCCCc-----eecCccccch
Q 028603 45 PDFPCPYCYE--DFDIASL-CSHLEDEHSCESKV-----TVCPICSVKV 85 (206)
Q Consensus 45 ~~F~CPfC~e--~fD~~~L-~~H~~eeH~~e~k~-----vVCPICa~~v 85 (206)
.+-.||+||+ -+--... |.|+-=+-|..++. -.||-|.+.+
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 4444555 77855554443333 3788887754
No 122
>PF14279 HNH_5: HNH endonuclease
Probab=35.66 E-value=8.5 Score=28.22 Aligned_cols=35 Identities=26% Similarity=0.601 Sum_probs=22.0
Q ss_pred CCCCCCCCCHHHHHHHhhhhccC--------CCCceecCccccchhhh
Q 028603 49 CPYCYEDFDIASLCSHLEDEHSC--------ESKVTVCPICSVKVARD 88 (206)
Q Consensus 49 CPfC~e~fD~~~L~~H~~eeH~~--------e~k~vVCPICa~~vs~d 88 (206)
|.||.++++....- +||-. ..+. ||--|-...+..
T Consensus 1 Ci~C~~~~~~~~~s----~EHIIP~sLGG~~~~~~-vC~~CN~~~g~~ 43 (71)
T PF14279_consen 1 CIYCNKEKSESNFS----EEHIIPESLGGKLKINN-VCDKCNNKFGSK 43 (71)
T ss_pred CccCCCCCCccCCC----ccccCchhcCCcccccc-hhHHHhHHHhHH
Confidence 89999976654321 45544 2233 888888776553
No 123
>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=35.64 E-value=28 Score=22.26 Aligned_cols=21 Identities=29% Similarity=0.585 Sum_probs=13.8
Q ss_pred CceecCccccch-hhhHhhhhh
Q 028603 74 KVTVCPICSVKV-ARDMLSHIT 94 (206)
Q Consensus 74 k~vVCPICa~~v-s~d~l~HL~ 94 (206)
..+.||.|.-.| ..-|+.||-
T Consensus 3 ~~~~C~nC~R~v~a~RfA~HLe 24 (33)
T PF08209_consen 3 PYVECPNCGRPVAASRFAPHLE 24 (33)
T ss_dssp -EEE-TTTSSEEEGGGHHHHHH
T ss_pred CeEECCCCcCCcchhhhHHHHH
Confidence 347899998876 456887773
No 124
>PF14353 CpXC: CpXC protein
Probab=35.42 E-value=16 Score=28.55 Aligned_cols=29 Identities=28% Similarity=0.438 Sum_probs=19.0
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCcee
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTV 77 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vV 77 (206)
..|+||.||..+-+ .+--.+|-.+.+.++
T Consensus 37 ~~~~CP~Cg~~~~~----~~p~lY~D~~~~~~i 65 (128)
T PF14353_consen 37 FSFTCPSCGHKFRL----EYPLLYHDPEKKFMI 65 (128)
T ss_pred CEEECCCCCCceec----CCCEEEEcCCCCEEE
Confidence 47999999996543 344556666655543
No 125
>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=35.14 E-value=22 Score=23.45 Aligned_cols=10 Identities=40% Similarity=0.972 Sum_probs=8.2
Q ss_pred CcccCCCCCC
Q 028603 45 PDFPCPYCYE 54 (206)
Q Consensus 45 ~~F~CPfC~e 54 (206)
..|.||+||-
T Consensus 17 ~g~~CP~Cg~ 26 (46)
T PF12760_consen 17 DGFVCPHCGS 26 (46)
T ss_pred CCCCCCCCCC
Confidence 4589999986
No 126
>PHA02929 N1R/p28-like protein; Provisional
Probab=34.97 E-value=7.1 Score=34.89 Aligned_cols=43 Identities=23% Similarity=0.483 Sum_probs=24.6
Q ss_pred CCcccCCCCCCCCCHH----------HHHHHhhhhccC---CCCceecCccccchh
Q 028603 44 RPDFPCPYCYEDFDIA----------SLCSHLEDEHSC---ESKVTVCPICSVKVA 86 (206)
Q Consensus 44 r~~F~CPfC~e~fD~~----------~L~~H~~eeH~~---e~k~vVCPICa~~vs 86 (206)
.....||.|.+.+... .=|.|.--..+. -.....||+|...+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 3467999999965432 124553222221 123468999987653
No 127
>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=34.88 E-value=28 Score=28.82 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=14.8
Q ss_pred CcccCCCCCC---CCCHHHHHHHh
Q 028603 45 PDFPCPYCYE---DFDIASLCSHL 65 (206)
Q Consensus 45 ~~F~CPfC~e---~fD~~~L~~H~ 65 (206)
..|.||-||. .+|-..+..=+
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i~~l 150 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAIEKL 150 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHHHHH
Confidence 4799999998 55655555433
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=33.89 E-value=13 Score=25.95 Aligned_cols=45 Identities=24% Similarity=0.558 Sum_probs=28.7
Q ss_pred CCCCCCCCC-CCCCcccCCCCCC--CCCHHHHHHHhhhhccCCCCceecCccccchh
Q 028603 33 SIDDFEVED-DVRPDFPCPYCYE--DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 33 ~~d~~e~dd-d~r~~F~CPfC~e--~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs 86 (206)
.++|++.++ +..-+|+|+ ||. .+....|-.+ .-.|-|+-|+-.+.
T Consensus 4 ~l~d~~~~~~~~~~~y~CR-CG~~f~i~e~~l~~~--------~~iv~C~sCSL~I~ 51 (55)
T PF05207_consen 4 SLDDMEFDEEEGVYSYPCR-CGGEFEISEEDLEEG--------EVIVQCDSCSLWIR 51 (55)
T ss_dssp ETTTSEEETTTTEEEEEET-TSSEEEEEHHHHHCT----------EEEETTTTEEEE
T ss_pred EhhhceecCCCCEEEEcCC-CCCEEEEcchhccCc--------CEEEECCCCccEEE
Confidence 345544332 234689994 988 7777777665 34578999987653
No 129
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=33.64 E-value=14 Score=31.84 Aligned_cols=22 Identities=27% Similarity=0.682 Sum_probs=0.0
Q ss_pred ceecCccccch-hhhHhhhhhcc
Q 028603 75 VTVCPICSVKV-ARDMLSHITLQ 96 (206)
Q Consensus 75 ~vVCPICa~~v-s~d~l~HL~~q 96 (206)
-++||||-.+| ...|-.||+..
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi~ 190 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRIE 190 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 37999999986 66899998763
No 130
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.61 E-value=17 Score=23.80 Aligned_cols=10 Identities=30% Similarity=0.657 Sum_probs=7.2
Q ss_pred ceecCccccc
Q 028603 75 VTVCPICSVK 84 (206)
Q Consensus 75 ~vVCPICa~~ 84 (206)
..+||.|-..
T Consensus 20 ~~vC~~Cg~~ 29 (52)
T smart00661 20 RFVCRKCGYE 29 (52)
T ss_pred EEECCcCCCe
Confidence 5788888643
No 131
>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=33.34 E-value=16 Score=28.86 Aligned_cols=38 Identities=26% Similarity=0.531 Sum_probs=21.3
Q ss_pred ccCCCCCCCCCHHHHHHHhhhh-ccCC-CC-ceecCccccchhh
Q 028603 47 FPCPYCYEDFDIASLCSHLEDE-HSCE-SK-VTVCPICSVKVAR 87 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~ee-H~~e-~k-~vVCPICa~~vs~ 87 (206)
-.|||||....+. ..-+-+ |..+ .. .=+|+-|-+.|+.
T Consensus 3 ~~CpYCg~~~~l~---~~~~iYg~~~~~~~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELV---DGSEIYGHRYDDGPYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEc---ccchhcCccCCCCceeEECCCCCceeee
Confidence 3699999833222 122222 2221 12 2689999999854
No 132
>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=33.26 E-value=19 Score=27.65 Aligned_cols=8 Identities=63% Similarity=1.767 Sum_probs=5.8
Q ss_pred ccCCCCCC
Q 028603 47 FPCPYCYE 54 (206)
Q Consensus 47 F~CPfC~e 54 (206)
.+||+||.
T Consensus 2 I~CP~CG~ 9 (84)
T TIGR01374 2 IPCPYCGP 9 (84)
T ss_pred ccCCCCCC
Confidence 46888885
No 133
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=33.19 E-value=14 Score=38.09 Aligned_cols=41 Identities=24% Similarity=0.430 Sum_probs=28.7
Q ss_pred CCCCcccCCCCCCCC----CHHHHHHHhhhhccCCCCceecCccccc
Q 028603 42 DVRPDFPCPYCYEDF----DIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 42 d~r~~F~CPfC~e~f----D~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
++...+.||.|+..+ +...|.||-...+ +...-.||=|-..
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 455679999998733 3356666655544 5667799999876
No 134
>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=33.04 E-value=7.6 Score=29.93 Aligned_cols=38 Identities=29% Similarity=0.679 Sum_probs=12.1
Q ss_pred cCCCCCCCCCHHHHH-HHhhhhccC-----------CCCceecCccccch
Q 028603 48 PCPYCYEDFDIASLC-SHLEDEHSC-----------ESKVTVCPICSVKV 85 (206)
Q Consensus 48 ~CPfC~e~fD~~~L~-~H~~eeH~~-----------e~k~vVCPICa~~v 85 (206)
.||+|++.+...++. .=|..-|.+ +.+.-+|++|..+.
T Consensus 16 ~C~~C~~~i~~~~~~~~~C~~GH~w~RC~lT~l~i~~~~~r~C~~C~~~~ 65 (99)
T PF12660_consen 16 KCPICGAPIPFDDLDEAQCENGHVWPRCALTFLPIQTPGVRVCPVCGRRA 65 (99)
T ss_dssp -------------SSEEE-TTS-EEEB-SSS-SBS-SS-EEE-TTT--EE
T ss_pred cccccccccccCCcCEeECCCCCEEeeeeeeeeeeccCCeeEcCCCCCEE
Confidence 699999977766543 347777765 55567899997664
No 135
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=32.92 E-value=36 Score=26.18 Aligned_cols=36 Identities=25% Similarity=0.555 Sum_probs=26.7
Q ss_pred ccCCCCCC-----CCCHHHHHHHhhhhccC------CCCceecCcccc
Q 028603 47 FPCPYCYE-----DFDIASLCSHLEDEHSC------ESKVTVCPICSV 83 (206)
Q Consensus 47 F~CPfC~e-----~fD~~~L~~H~~eeH~~------e~k~vVCPICa~ 83 (206)
=.||-|-. .+ +-++|.|+--.|+. ..+.+-||+|..
T Consensus 32 g~Cp~Ck~PgDdCPL-v~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq 78 (84)
T KOG1493|consen 32 GCCPDCKLPGDDCPL-VWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQ 78 (84)
T ss_pred CcCCCCcCCCCCCcc-HHHHHHHHHHHHHHHHHhcCccccccCCcchh
Confidence 36777743 33 77899999988875 445689999964
No 136
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.85 E-value=9 Score=36.19 Aligned_cols=39 Identities=26% Similarity=0.586 Sum_probs=30.6
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCC---------CceecCccccch
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCES---------KVTVCPICSVKV 85 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~---------k~vVCPICa~~v 85 (206)
+.|-.|-|+|...+.+.++-=.|.|-. ..-.||||-..+
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di 277 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDI 277 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcC
Confidence 999999999999888877777777622 235799997754
No 137
>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=32.81 E-value=19 Score=35.22 Aligned_cols=48 Identities=33% Similarity=0.453 Sum_probs=33.6
Q ss_pred CCCHHHHHHHhhhhccCCC-----------------CceecCccccch--hhhHhhhhhccccchhh
Q 028603 55 DFDIASLCSHLEDEHSCES-----------------KVTVCPICSVKV--ARDMLSHITLQHGHLFK 102 (206)
Q Consensus 55 ~fD~~~L~~H~~eeH~~e~-----------------k~vVCPICa~~v--s~d~l~HL~~qH~~~~k 102 (206)
.+.+..|..|+...|..++ +.-+||+|..+- ...+..|+...|-..++
T Consensus 20 kVsi~eL~sy~~~~~~~~a~~~Lseal~fak~n~sWrFWiCp~CskkF~d~~~~~~H~~~eH~~~l~ 86 (466)
T PF04780_consen 20 KVSIDELKSYYESVYDREAADALSEALSFAKENKSWRFWICPRCSKKFSDAESCLSHMEQEHPAGLK 86 (466)
T ss_pred eeEHHHHHHHHHhccchHHHHHHHHHHHHHHhcCceeEeeCCcccceeCCHHHHHHHHHHhhhhhcC
Confidence 4566666666666654322 235799999764 66899999999977663
No 138
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=32.73 E-value=22 Score=25.94 Aligned_cols=26 Identities=35% Similarity=0.828 Sum_probs=16.5
Q ss_pred eecCccccch--hhhHhhhhhccccchh
Q 028603 76 TVCPICSVKV--ARDMLSHITLQHGHLF 101 (206)
Q Consensus 76 vVCPICa~~v--s~d~l~HL~~qH~~~~ 101 (206)
..||-|.+.. ..+.++|.+-.|+..+
T Consensus 18 lrCPRC~~~FR~~K~Y~RHVNKaH~~~~ 45 (65)
T COG4049 18 LRCPRCGMVFRRRKDYIRHVNKAHGWLF 45 (65)
T ss_pred eeCCchhHHHHHhHHHHHHhhHHhhhhh
Confidence 3455554432 4577788888887766
No 139
>PHA00733 hypothetical protein
Probab=32.21 E-value=44 Score=26.77 Aligned_cols=25 Identities=24% Similarity=0.483 Sum_probs=21.6
Q ss_pred cccCCCCCCC-CCHHHHHHHhhhhcc
Q 028603 46 DFPCPYCYED-FDIASLCSHLEDEHS 70 (206)
Q Consensus 46 ~F~CPfC~e~-fD~~~L~~H~~eeH~ 70 (206)
.|.|+.|++. -....|..|+...|.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHHHhcC
Confidence 5999999994 566889999999996
No 140
>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=32.19 E-value=19 Score=28.23 Aligned_cols=19 Identities=21% Similarity=0.627 Sum_probs=12.7
Q ss_pred CcccCCCCCC-CCCHHHHHH
Q 028603 45 PDFPCPYCYE-DFDIASLCS 63 (206)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~ 63 (206)
..|.||+|.. +=.+..+..
T Consensus 23 ~D~~Cp~C~~~~~~~~~~~~ 42 (178)
T cd03019 23 FSYGCPHCYNFEPILEAWVK 42 (178)
T ss_pred ECCCCcchhhhhHHHHHHHH
Confidence 3699999988 544444433
No 141
>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=31.90 E-value=15 Score=31.56 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=0.0
Q ss_pred cccCCCCCCCCCHHHHHHHhhhh
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDE 68 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~ee 68 (206)
...||+||+-+-+..+-+|++-+
T Consensus 168 ~~~cPitGe~IP~~e~~eHmRi~ 190 (229)
T PF12230_consen 168 MIICPITGEMIPADEMDEHMRIE 190 (229)
T ss_dssp -----------------------
T ss_pred ccccccccccccccccccccccc
Confidence 47999999999999999999765
No 142
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.56 E-value=25 Score=25.78 Aligned_cols=13 Identities=38% Similarity=0.976 Sum_probs=7.6
Q ss_pred CCCceecCccccc
Q 028603 72 ESKVTVCPICSVK 84 (206)
Q Consensus 72 e~k~vVCPICa~~ 84 (206)
+.+.|+||-|..+
T Consensus 45 ~~gev~CPYC~t~ 57 (62)
T COG4391 45 DEGEVVCPYCSTR 57 (62)
T ss_pred CCCcEecCccccE
Confidence 4555666666553
No 143
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=31.50 E-value=25 Score=33.60 Aligned_cols=40 Identities=23% Similarity=0.517 Sum_probs=31.5
Q ss_pred cccCCC--CCC-CCCHHHHHHHhhhhccC-----------------CCCceecCccccch
Q 028603 46 DFPCPY--CYE-DFDIASLCSHLEDEHSC-----------------ESKVTVCPICSVKV 85 (206)
Q Consensus 46 ~F~CPf--C~e-~fD~~~L~~H~~eeH~~-----------------e~k~vVCPICa~~v 85 (206)
-|.||. |.+ --.+-+|.-|...-|+. +.|.-+|+||..+-
T Consensus 349 pykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 349 PYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred eecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhh
Confidence 499987 777 77888999999988832 33567899999875
No 144
>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=31.43 E-value=6.1 Score=30.90 Aligned_cols=30 Identities=23% Similarity=0.556 Sum_probs=18.7
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
..+..+.|.-||..|++.... ..||-|-..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~-------------~~CP~Cgs~ 95 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFD-------------FSCPRCGSP 95 (113)
T ss_dssp EE--EEEETTTS-EEECHHCC-------------HH-SSSSSS
T ss_pred ecCCcEECCCCCCEEecCCCC-------------CCCcCCcCC
Confidence 446789999999977765542 239999765
No 145
>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=31.36 E-value=22 Score=35.04 Aligned_cols=42 Identities=29% Similarity=0.570 Sum_probs=26.5
Q ss_pred CCcccCCCCCCCCCH--HHHHHHhhhhccCCCCceecCccccchhh
Q 028603 44 RPDFPCPYCYEDFDI--ASLCSHLEDEHSCESKVTVCPICSVKVAR 87 (206)
Q Consensus 44 r~~F~CPfC~e~fD~--~~L~~H~~eeH~~e~k~vVCPICa~~vs~ 87 (206)
+-..+||-||+.+.+ ..|.- .++...+.-..+||-|-..+..
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w--~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKW--DKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEEccCCCCCCCccccccceee--cCCCCccceEEECCCCcCCCCH
Confidence 557899999994443 33322 2112334445799999998854
No 146
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.00 E-value=23 Score=34.01 Aligned_cols=50 Identities=22% Similarity=0.486 Sum_probs=0.0
Q ss_pred CCCCCcccCCCCCCCCCHHHH-------HHHhhhhccCCCCceecCccccchhhhHhhh
Q 028603 41 DDVRPDFPCPYCYEDFDIASL-------CSHLEDEHSCESKVTVCPICSVKVARDMLSH 92 (206)
Q Consensus 41 dd~r~~F~CPfC~e~fD~~~L-------~~H~~eeH~~e~k~vVCPICa~~vs~d~l~H 92 (206)
++++..|.||.|.+.|....+ |..|-.++-.... .||+|...+...-+++
T Consensus 21 ~~Le~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~--~CP~Cr~~~~~~~Lr~ 77 (397)
T TIGR00599 21 YPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQP--KCPLCRAEDQESKLRS 77 (397)
T ss_pred cccccccCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCC--CCCCCCCccccccCcc
No 147
>PRK10220 hypothetical protein; Provisional
Probab=30.95 E-value=33 Score=27.72 Aligned_cols=12 Identities=25% Similarity=0.855 Sum_probs=7.7
Q ss_pred CCceecCccccc
Q 028603 73 SKVTVCPICSVK 84 (206)
Q Consensus 73 ~k~vVCPICa~~ 84 (206)
....|||-|+--
T Consensus 18 ~~~~vCpeC~hE 29 (111)
T PRK10220 18 NGMYICPECAHE 29 (111)
T ss_pred CCeEECCcccCc
Confidence 335678888654
No 148
>PRK04023 DNA polymerase II large subunit; Validated
Probab=30.79 E-value=21 Score=38.29 Aligned_cols=37 Identities=19% Similarity=0.360 Sum_probs=18.5
Q ss_pred CcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 45 PDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 45 ~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
..|.||.||+.-...--|..|... .....||-|-..+
T Consensus 637 ~~frCP~CG~~Te~i~fCP~CG~~----~~~y~CPKCG~El 673 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRCGIE----VEEDECEKCGREP 673 (1121)
T ss_pred CcccCCCCCCCCCcceeCccccCc----CCCCcCCCCCCCC
Confidence 346666666643333445555222 2234577776654
No 149
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=30.41 E-value=26 Score=35.59 Aligned_cols=54 Identities=26% Similarity=0.560 Sum_probs=34.0
Q ss_pred CCCCCCcccCCCCCC-CCC-HHHHHHH-----hhh---hccCCCCceecCccccchhhhHhhhh
Q 028603 40 EDDVRPDFPCPYCYE-DFD-IASLCSH-----LED---EHSCESKVTVCPICSVKVARDMLSHI 93 (206)
Q Consensus 40 ddd~r~~F~CPfC~e-~fD-~~~L~~H-----~~e---eH~~e~k~vVCPICa~~vs~d~l~HL 93 (206)
+||-...--|-+|.+ -=| +..-|.| |.. +-..+..+|-||+|.-.++.|+..|-
T Consensus 530 ~~enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a 593 (791)
T KOG1002|consen 530 PDENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA 593 (791)
T ss_pred CccccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence 345566788999987 222 3333333 332 22347778999999988776655543
No 150
>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=30.31 E-value=32 Score=28.47 Aligned_cols=32 Identities=19% Similarity=0.359 Sum_probs=22.8
Q ss_pred CCCCcccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccchh
Q 028603 42 DVRPDFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 42 d~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs 86 (206)
++-....||-||. =||+ ....+|||-|-....
T Consensus 5 elGtKr~Cp~cg~kFYDL-------------nk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDL-------------NRRPAVSPYTGEQFP 37 (129)
T ss_pred hhCccccCCCcCcccccc-------------CCCCccCCCcCCccC
Confidence 4456789999998 4442 245799999987653
No 151
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=29.96 E-value=38 Score=28.69 Aligned_cols=19 Identities=37% Similarity=0.800 Sum_probs=13.2
Q ss_pred CcccCCCCCC---CCCHHHHHH
Q 028603 45 PDFPCPYCYE---DFDIASLCS 63 (206)
Q Consensus 45 ~~F~CPfC~e---~fD~~~L~~ 63 (206)
..|.||.||. .+|-..+..
T Consensus 135 ~~F~Cp~Cg~~L~~~dn~~~~~ 156 (178)
T PRK06266 135 YGFRCPQCGEMLEEYDNSELIK 156 (178)
T ss_pred cCCcCCCCCCCCeecccHHHHH
Confidence 4799999998 445444443
No 152
>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=29.89 E-value=17 Score=26.32 Aligned_cols=11 Identities=27% Similarity=0.966 Sum_probs=8.4
Q ss_pred CCcccCCCCCC
Q 028603 44 RPDFPCPYCYE 54 (206)
Q Consensus 44 r~~F~CPfC~e 54 (206)
...+.|-+||+
T Consensus 3 k~~~~C~~Cg~ 13 (69)
T PF09706_consen 3 KKKYNCIFCGE 13 (69)
T ss_pred CCCCcCcCCCC
Confidence 34788999994
No 153
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=29.21 E-value=43 Score=25.44 Aligned_cols=30 Identities=30% Similarity=0.523 Sum_probs=24.4
Q ss_pred CCCCceecCccccch-hhhHhhhhhccccch
Q 028603 71 CESKVTVCPICSVKV-ARDMLSHITLQHGHL 100 (206)
Q Consensus 71 ~e~k~vVCPICa~~v-s~d~l~HL~~qH~~~ 100 (206)
.+.+.+||-.|-.-| ...+.+||..+|...
T Consensus 7 ~~~~vlIC~~C~~av~~~~v~~HL~~~H~~~ 37 (109)
T PF12013_consen 7 PEYRVLICRQCQYAVQPSEVESHLRKRHHIL 37 (109)
T ss_pred CcCCEEEeCCCCcccCchHHHHHHHHhcccc
Confidence 466789999997765 589999999888765
No 154
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=29.12 E-value=6.2 Score=30.43 Aligned_cols=21 Identities=29% Similarity=0.641 Sum_probs=16.3
Q ss_pred CcccCCCCCC-CCCHHHHHHHh
Q 028603 45 PDFPCPYCYE-DFDIASLCSHL 65 (206)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~ 65 (206)
..|.||+|.. .-.+..|..+.
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 4699999999 77777888775
No 155
>PF14968 CCDC84: Coiled coil protein 84
Probab=28.70 E-value=28 Score=32.78 Aligned_cols=26 Identities=23% Similarity=0.428 Sum_probs=19.4
Q ss_pred CCCCCcccCCCCCCCCCHH-------HHHHHhh
Q 028603 41 DDVRPDFPCPYCYEDFDIA-------SLCSHLE 66 (206)
Q Consensus 41 dd~r~~F~CPfC~e~fD~~-------~L~~H~~ 66 (206)
.+-+..|=|+||+.++... ++..|+-
T Consensus 53 ~~~~~~fWC~fC~~ev~~~~s~~~~~~ai~HLa 85 (336)
T PF14968_consen 53 PEHRNRFWCVFCDCEVREHDSSFACGGAIEHLA 85 (336)
T ss_pred ccccceeEeeCccchhhhccchhhhccHHhhcC
Confidence 3567789999999977755 6666654
No 156
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.69 E-value=16 Score=32.74 Aligned_cols=45 Identities=27% Similarity=0.594 Sum_probs=31.8
Q ss_pred CCcccCCCCCC--CCCHHHHHHHhh-------hhccCCCCceecCccccchhhhH
Q 028603 44 RPDFPCPYCYE--DFDIASLCSHLE-------DEHSCESKVTVCPICSVKVARDM 89 (206)
Q Consensus 44 r~~F~CPfC~e--~fD~~~L~~H~~-------eeH~~e~k~vVCPICa~~vs~d~ 89 (206)
-..|.|-.|.+ .==|..||-|+- --|. ..+...||||-+.|+.+-
T Consensus 45 ~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~-~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 45 GGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQT-RPNSKECPVCKAEVSIDT 98 (230)
T ss_pred CCceeeeeeccccCCCEEeecccceehHHHHHHHhh-cCCCeeCCccccccccce
Confidence 35799999988 556788998863 1222 244568999999986543
No 157
>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=28.22 E-value=15 Score=28.12 Aligned_cols=7 Identities=57% Similarity=1.497 Sum_probs=4.0
Q ss_pred cCCCCCC
Q 028603 48 PCPYCYE 54 (206)
Q Consensus 48 ~CPfC~e 54 (206)
+|||||+
T Consensus 3 ~CP~CG~ 9 (84)
T PF04267_consen 3 PCPHCGP 9 (84)
T ss_dssp EETTTEE
T ss_pred cCCCCCc
Confidence 4666655
No 158
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.06 E-value=38 Score=34.75 Aligned_cols=30 Identities=30% Similarity=0.433 Sum_probs=26.0
Q ss_pred CCCcccCCCCCC-CCCHHHHHHHhhhhccCC
Q 028603 43 VRPDFPCPYCYE-DFDIASLCSHLEDEHSCE 72 (206)
Q Consensus 43 ~r~~F~CPfC~e-~fD~~~L~~H~~eeH~~e 72 (206)
.+.---|+||.+ -||..+|..|+..+|.+.
T Consensus 179 ~rGhp~C~~C~~~fld~~el~rH~~~~h~~c 209 (669)
T KOG2231|consen 179 CRGHPLCKFCHERFLDDDELYRHLRFDHEFC 209 (669)
T ss_pred ccCCccchhhhhhhccHHHHHHhhccceehe
Confidence 345678999999 999999999999999863
No 159
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=27.86 E-value=25 Score=27.06 Aligned_cols=37 Identities=32% Similarity=0.535 Sum_probs=24.6
Q ss_pred cCCCCCC-CCCH---HHHHHHhhhhccC------CCCceecCccccc
Q 028603 48 PCPYCYE-DFDI---ASLCSHLEDEHSC------ESKVTVCPICSVK 84 (206)
Q Consensus 48 ~CPfC~e-~fD~---~~L~~H~~eeH~~------e~k~vVCPICa~~ 84 (206)
.||-|-. +-|- -+-|.|.--.|+. +..+..||+|...
T Consensus 34 ~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~ 80 (85)
T PF12861_consen 34 CCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQP 80 (85)
T ss_pred CCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCe
Confidence 4888866 5442 2457777777764 3456899999753
No 160
>KOG4696 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.82 E-value=38 Score=32.13 Aligned_cols=24 Identities=29% Similarity=0.847 Sum_probs=20.3
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhcc
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHS 70 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~ 70 (206)
+.-||||.-.+...+.|.|++ .|-
T Consensus 2 e~iCP~CkLsv~~~~m~~Hie-aHF 25 (393)
T KOG4696|consen 2 EIICPFCKLSVNYDEMCFHIE-AHF 25 (393)
T ss_pred cccccceecccCHHHHHHHHH-hhc
Confidence 457999988999999999998 444
No 161
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=27.39 E-value=31 Score=29.68 Aligned_cols=13 Identities=46% Similarity=0.958 Sum_probs=10.5
Q ss_pred ccCCCCCCCCCHH
Q 028603 47 FPCPYCYEDFDIA 59 (206)
Q Consensus 47 F~CPfC~e~fD~~ 59 (206)
-+||+||.-+|-.
T Consensus 155 P~CPlCg~PlDP~ 167 (171)
T PF11290_consen 155 PPCPLCGEPLDPE 167 (171)
T ss_pred CCCCCCCCCCCCC
Confidence 6899999977743
No 162
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.35 E-value=37 Score=32.11 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=20.0
Q ss_pred CCCCCcccCCCCCCCCCHHHHHHH
Q 028603 41 DDVRPDFPCPYCYEDFDIASLCSH 64 (206)
Q Consensus 41 dd~r~~F~CPfC~e~fD~~~L~~H 64 (206)
+.+...|+||.|+..|-..+|-.|
T Consensus 15 ~q~~~~fpc~ic~r~f~~~~L~kh 38 (351)
T KOG3940|consen 15 AQMQMRFPCRICQREFRRRELMKH 38 (351)
T ss_pred ccccccccccccccchhhhhhhcc
Confidence 456679999999998888888776
No 163
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=27.22 E-value=45 Score=28.56 Aligned_cols=41 Identities=15% Similarity=0.326 Sum_probs=26.2
Q ss_pred ccCCCCCC---CCCHHHHHHHhhhhccCCC-CceecCccccc--hhh
Q 028603 47 FPCPYCYE---DFDIASLCSHLEDEHSCES-KVTVCPICSVK--VAR 87 (206)
Q Consensus 47 F~CPfC~e---~fD~~~L~~H~~eeH~~e~-k~vVCPICa~~--vs~ 87 (206)
=.||+|+. .+...+...-+.+.|.... ..-+||.|-.. +|.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~Gs 144 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGS 144 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCch
Confidence 36999987 5555555555555555433 34679999876 454
No 164
>PF14369 zf-RING_3: zinc-finger
Probab=27.05 E-value=30 Score=22.06 Aligned_cols=9 Identities=44% Similarity=1.228 Sum_probs=7.7
Q ss_pred cCCCCCCCC
Q 028603 48 PCPYCYEDF 56 (206)
Q Consensus 48 ~CPfC~e~f 56 (206)
.||.|+.+|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 799998866
No 165
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=26.75 E-value=22 Score=34.76 Aligned_cols=18 Identities=28% Similarity=0.637 Sum_probs=13.8
Q ss_pred ccCCCCceecCccccchh
Q 028603 69 HSCESKVTVCPICSVKVA 86 (206)
Q Consensus 69 H~~e~k~vVCPICa~~vs 86 (206)
.-.+++.-|||||...||
T Consensus 31 ~~~~PNt~vcpv~lg~PG 48 (474)
T PRK05477 31 FGAEPNTNVCPVCLGLPG 48 (474)
T ss_pred cCCCCCCCcCccccCCCC
Confidence 334678899999999863
No 166
>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=26.58 E-value=23 Score=23.52 Aligned_cols=9 Identities=44% Similarity=1.180 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 028603 46 DFPCPYCYE 54 (206)
Q Consensus 46 ~F~CPfC~e 54 (206)
.-.||||+.
T Consensus 29 ~~~CpYCg~ 37 (40)
T PF10276_consen 29 PVVCPYCGT 37 (40)
T ss_dssp EEEETTTTE
T ss_pred eEECCCCCC
Confidence 678999985
No 167
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=26.25 E-value=32 Score=25.58 Aligned_cols=8 Identities=50% Similarity=1.464 Sum_probs=5.8
Q ss_pred ccCCCCCC
Q 028603 47 FPCPYCYE 54 (206)
Q Consensus 47 F~CPfC~e 54 (206)
|.||+||.
T Consensus 2 m~CP~Cg~ 9 (72)
T PRK09678 2 FHCPLCQH 9 (72)
T ss_pred ccCCCCCC
Confidence 56777776
No 168
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=26.10 E-value=50 Score=28.37 Aligned_cols=32 Identities=19% Similarity=0.531 Sum_probs=22.2
Q ss_pred CCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 44 RPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 44 r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
...|.||-|..-+...+-+.+- -.||.|-+.+
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~~~----------F~Cp~Cg~~L 142 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAMELG----------FTCPKCGEDL 142 (176)
T ss_pred CCceeCCCCCCcccHHHHHHhC----------CCCCCCCchh
Confidence 3579999998844444433332 6999998876
No 169
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.07 E-value=60 Score=20.65 Aligned_cols=31 Identities=19% Similarity=0.591 Sum_probs=17.1
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCcccc
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSV 83 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~ 83 (206)
+.||-|+..|++.+- .=+.....|.||.|..
T Consensus 3 i~Cp~C~~~y~i~d~------~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDE------KIPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHH------HCCCCCcEEECCCCCC
Confidence 467777774444321 1123445677777754
No 170
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=25.77 E-value=38 Score=32.62 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=8.6
Q ss_pred CCCcccCCCCCC
Q 028603 43 VRPDFPCPYCYE 54 (206)
Q Consensus 43 ~r~~F~CPfC~e 54 (206)
....|.|+.||-
T Consensus 422 ~~~~~~c~~c~~ 433 (479)
T PRK05452 422 LGPRMQCSVCQW 433 (479)
T ss_pred CCCeEEECCCCe
Confidence 355788888865
No 171
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=25.53 E-value=40 Score=18.73 Aligned_cols=7 Identities=43% Similarity=1.217 Sum_probs=3.2
Q ss_pred cCccccc
Q 028603 78 CPICSVK 84 (206)
Q Consensus 78 CPICa~~ 84 (206)
|.||-..
T Consensus 3 C~~C~~~ 9 (25)
T PF12874_consen 3 CDICNKS 9 (25)
T ss_dssp ETTTTEE
T ss_pred CCCCCCC
Confidence 4555443
No 172
>PF10023 DUF2265: Predicted aminopeptidase (DUF2265); InterPro: IPR014553 This group represents a predicted aminopeptidase.
Probab=25.53 E-value=29 Score=32.65 Aligned_cols=35 Identities=31% Similarity=0.450 Sum_probs=23.6
Q ss_pred chhhhhhhhhhhhCCCCCCCCCCCCCCCCCCchhhhhcc
Q 028603 124 GRDLREAHLQVLLGGSGYRSSNANISNAATDPFLSSLIL 162 (206)
Q Consensus 124 ~k~lre~~lq~llgg~~~~~~~~~~s~~~pDPLLSsFi~ 162 (206)
.+.||+..|...+||-+-.|+.+ --.|||||+||.
T Consensus 125 a~~L~~~GlDv~v~gV~AYSTLG----wF~DPlLSt~l~ 159 (337)
T PF10023_consen 125 AAELRAQGLDVYVGGVPAYSTLG----WFDDPLLSTMLR 159 (337)
T ss_pred HHHHHHcCCceeEeccccccccc----ccCCcccccccC
Confidence 44666667777777764333222 358999999997
No 173
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=25.50 E-value=37 Score=22.98 Aligned_cols=33 Identities=18% Similarity=0.539 Sum_probs=19.7
Q ss_pred CCCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCcc
Q 028603 41 DDVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPIC 81 (206)
Q Consensus 41 dd~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPIC 81 (206)
.....-+.||.||-++...-= .+. .+...||.|
T Consensus 23 s~~~v~W~C~~Cgh~w~~~v~-------~R~-~~~~~CP~C 55 (55)
T PF14311_consen 23 SNKKVWWKCPKCGHEWKASVN-------DRT-RRGKGCPYC 55 (55)
T ss_pred CCCEEEEECCCCCCeeEccHh-------hhc-cCCCCCCCC
Confidence 344567999999775543211 011 445689988
No 174
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.38 E-value=21 Score=28.19 Aligned_cols=31 Identities=29% Similarity=0.612 Sum_probs=21.2
Q ss_pred CCCCcccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 42 DVRPDFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 42 d~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
+.+..+.|+-||..|..... ....||-|-..
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNAL------------DYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCccccCCc------------cCCcCcCCCCC
Confidence 45678999999986655422 22459999764
No 175
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=25.05 E-value=21 Score=24.29 Aligned_cols=17 Identities=41% Similarity=0.960 Sum_probs=11.4
Q ss_pred cccCCCCCC-CCCHHHHH
Q 028603 46 DFPCPYCYE-DFDIASLC 62 (206)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~ 62 (206)
.|.||+|.. .-.+..+.
T Consensus 6 d~~Cp~C~~~~~~l~~~~ 23 (98)
T cd02972 6 DPLCPYCYLFEPELEKLL 23 (98)
T ss_pred CCCCHhHHhhhHHHHHHH
Confidence 588999988 44444443
No 176
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=24.91 E-value=14 Score=34.63 Aligned_cols=40 Identities=28% Similarity=0.497 Sum_probs=26.9
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhcc-CCCCceecCccccch
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHS-CESKVTVCPICSVKV 85 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~-~e~k~vVCPICa~~v 85 (206)
.-.||+|+.+--....|++|-.... .+..+.+|.+|-..+
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 3579999965555677777766554 577889999998875
No 177
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=24.34 E-value=56 Score=31.75 Aligned_cols=43 Identities=16% Similarity=0.397 Sum_probs=26.1
Q ss_pred HHHHHhhhhcc-CCCCceecCccccch--hhhHhhhhhccccchhh
Q 028603 60 SLCSHLEDEHS-CESKVTVCPICSVKV--ARDMLSHITLQHGHLFK 102 (206)
Q Consensus 60 ~L~~H~~eeH~-~e~k~vVCPICa~~v--s~d~l~HL~~qH~~~~k 102 (206)
.|..|..+.|- +.+-.-.|-+|...- |.++.+||+-+|+|-..
T Consensus 336 q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~f~~P 381 (467)
T KOG3608|consen 336 QMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHGFRLP 381 (467)
T ss_pred HHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhcccCC
Confidence 34444444442 223334566665543 77999999999998543
No 178
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=24.09 E-value=46 Score=30.44 Aligned_cols=43 Identities=19% Similarity=0.413 Sum_probs=29.3
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccchhhhHhhhhhccccc
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVKVARDMLSHITLQHGH 99 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~vs~d~l~HL~~qH~~ 99 (206)
..||.|+.. ++ ..+ ++....||--|-..+..+++.+---.+.|
T Consensus 2 ~~CpeCg~~-~~-------~~d--~~~ge~VC~~CG~Vi~~~~id~gpewr~f 44 (285)
T COG1405 2 MSCPECGST-NI-------ITD--YERGEIVCADCGLVLEDSLIDPGPEWRAF 44 (285)
T ss_pred CCCCCCCCc-cc-------eee--ccCCeEEeccCCEEeccccccCCCCcccc
Confidence 479999985 11 111 22567899999999988888765555545
No 179
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=23.88 E-value=18 Score=27.48 Aligned_cols=37 Identities=16% Similarity=0.321 Sum_probs=17.7
Q ss_pred CCCCCCCCCHHHHHHHhhhhc----cCCCCceecCccccch
Q 028603 49 CPYCYEDFDIASLCSHLEDEH----SCESKVTVCPICSVKV 85 (206)
Q Consensus 49 CPfC~e~fD~~~L~~H~~eeH----~~e~k~vVCPICa~~v 85 (206)
||+|+.+--+.....+.-+.- ..+....+||.|-...
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 899986322233322221110 0122335799997763
No 180
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.65 E-value=30 Score=37.99 Aligned_cols=35 Identities=31% Similarity=0.737 Sum_probs=17.1
Q ss_pred cccCCCCCC-CCCHHHHHHHhhhhccCCCCceecCccccch
Q 028603 46 DFPCPYCYE-DFDIASLCSHLEDEHSCESKVTVCPICSVKV 85 (206)
Q Consensus 46 ~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~vVCPICa~~v 85 (206)
.|.||-||. .+. ..|..|-.. .+. ..+||.|-+.+
T Consensus 667 ~rkCPkCG~~t~~--~fCP~CGs~--te~-vy~CPsCGaev 702 (1337)
T PRK14714 667 RRRCPSCGTETYE--NRCPDCGTH--TEP-VYVCPDCGAEV 702 (1337)
T ss_pred EEECCCCCCcccc--ccCcccCCc--CCC-ceeCccCCCcc
Confidence 477777777 332 244444432 111 23566665543
No 181
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.49 E-value=25 Score=27.69 Aligned_cols=11 Identities=18% Similarity=0.552 Sum_probs=5.9
Q ss_pred CCcccCCCCCC
Q 028603 44 RPDFPCPYCYE 54 (206)
Q Consensus 44 r~~F~CPfC~e 54 (206)
+..+.|+-|+.
T Consensus 68 p~~~~C~~Cg~ 78 (114)
T PRK03681 68 EAECWCETCQQ 78 (114)
T ss_pred CcEEEcccCCC
Confidence 44555555555
No 182
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=23.13 E-value=36 Score=28.49 Aligned_cols=32 Identities=22% Similarity=0.560 Sum_probs=18.5
Q ss_pred ccCCCCCCCCCHHHHHHHhhhhccCCCCc-----eecCccccc
Q 028603 47 FPCPYCYEDFDIASLCSHLEDEHSCESKV-----TVCPICSVK 84 (206)
Q Consensus 47 F~CPfC~e~fD~~~L~~H~~eeH~~e~k~-----vVCPICa~~ 84 (206)
..|||||.... |+.+.-.....+ --||-|.-.
T Consensus 1 m~cp~c~~~~~------~~~~s~~~~~~~~~~~~~~c~~c~~~ 37 (154)
T PRK00464 1 MRCPFCGHPDT------RVIDSRPAEDGNAIRRRRECLACGKR 37 (154)
T ss_pred CcCCCCCCCCC------EeEeccccCCCCceeeeeeccccCCc
Confidence 36999998432 233333333332 349999876
No 183
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=22.95 E-value=28 Score=34.68 Aligned_cols=21 Identities=29% Similarity=0.518 Sum_probs=16.0
Q ss_pred hhhccCCCCceecCccccchh
Q 028603 66 EDEHSCESKVTVCPICSVKVA 86 (206)
Q Consensus 66 ~eeH~~e~k~vVCPICa~~vs 86 (206)
..+.-.+++.-|||||...||
T Consensus 84 ~~~~g~~PNt~vcpvclg~PG 104 (544)
T PLN02751 84 PYNYGAEPNTTVCPVCMGLPG 104 (544)
T ss_pred CcccCCCCccCcCccccCCCC
Confidence 334455788899999999863
No 184
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=22.63 E-value=26 Score=29.79 Aligned_cols=41 Identities=22% Similarity=0.549 Sum_probs=26.0
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhc-----cCCC-CceecCccccchh
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEH-----SCES-KVTVCPICSVKVA 86 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH-----~~e~-k~vVCPICa~~vs 86 (206)
.-.||.|+..++..--..|++=.| .... +-+.|+-|-...|
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 457999999775432223777777 3322 4467999977544
No 185
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=22.42 E-value=66 Score=29.10 Aligned_cols=35 Identities=26% Similarity=0.399 Sum_probs=19.8
Q ss_pred CCCcccCCCCCCCCCHHHHHHHhhhhccCC--CCceecCccccchh
Q 028603 43 VRPDFPCPYCYEDFDIASLCSHLEDEHSCE--SKVTVCPICSVKVA 86 (206)
Q Consensus 43 ~r~~F~CPfC~e~fD~~~L~~H~~eeH~~e--~k~vVCPICa~~vs 86 (206)
.+...-||-|.- |-.-.|..+ ...-|||-|-+..+
T Consensus 189 ~~~alIC~~C~h---------hngl~~~~ek~~~efiC~~Cn~~n~ 225 (251)
T COG5415 189 PFKALICPQCHH---------HNGLYRLAEKPIIEFICPHCNHKND 225 (251)
T ss_pred chhhhccccccc---------cccccccccccchheecccchhhcC
Confidence 355677888854 112223332 22468999987653
No 186
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.38 E-value=46 Score=32.10 Aligned_cols=16 Identities=31% Similarity=0.756 Sum_probs=11.2
Q ss_pred CCcccCCCCCCCCCHH
Q 028603 44 RPDFPCPYCYEDFDIA 59 (206)
Q Consensus 44 r~~F~CPfC~e~fD~~ 59 (206)
..+|.||||-.+-+..
T Consensus 372 ~~sfKCPYCP~e~~~~ 387 (394)
T KOG2817|consen 372 SQSFKCPYCPVEQLAS 387 (394)
T ss_pred CeeeeCCCCCcccCHH
Confidence 3469999998755443
No 187
>PHA02540 61 DNA primase; Provisional
Probab=22.34 E-value=38 Score=31.78 Aligned_cols=10 Identities=40% Similarity=1.125 Sum_probs=8.8
Q ss_pred CcccCCCCCC
Q 028603 45 PDFPCPYCYE 54 (206)
Q Consensus 45 ~~F~CPfC~e 54 (206)
-.+.||||++
T Consensus 26 ~~~~CPf~~d 35 (337)
T PHA02540 26 YNFRCPICGD 35 (337)
T ss_pred EEecCCCCCC
Confidence 4789999998
No 188
>cd03024 DsbA_FrnE DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=21.92 E-value=23 Score=28.59 Aligned_cols=22 Identities=27% Similarity=0.671 Sum_probs=15.8
Q ss_pred CCcccCCCCCC-CCCHHHHHHHh
Q 028603 44 RPDFPCPYCYE-DFDIASLCSHL 65 (206)
Q Consensus 44 r~~F~CPfC~e-~fD~~~L~~H~ 65 (206)
-..|.||||+. .-.+..+....
T Consensus 4 ~~D~~cP~cyl~~~~l~~~~~~~ 26 (201)
T cd03024 4 WSDVVCPWCYIGKRRLEKALAEL 26 (201)
T ss_pred EecCcCccHHHHHHHHHHHHHhC
Confidence 45799999998 55666666554
No 189
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=21.44 E-value=51 Score=30.14 Aligned_cols=29 Identities=28% Similarity=0.559 Sum_probs=21.1
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
--.||-|++-+-..+|-.. .-|||-|-..
T Consensus 27 ~~~c~~c~~~~~~~~l~~~----------~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEAN----------LNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHhc----------CCCCCCCCCC
Confidence 4689999997766666432 3599999775
No 190
>TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit. The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both.
Probab=20.95 E-value=33 Score=33.55 Aligned_cols=15 Identities=27% Similarity=0.656 Sum_probs=13.0
Q ss_pred CCCceecCccccchh
Q 028603 72 ESKVTVCPICSVKVA 86 (206)
Q Consensus 72 e~k~vVCPICa~~vs 86 (206)
+++..|||||...||
T Consensus 34 ~PNt~v~pvclg~PG 48 (478)
T TIGR00133 34 PPNTNVCPVCLGLPG 48 (478)
T ss_pred CCCcccCccccCCCC
Confidence 688899999999873
No 191
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=20.87 E-value=58 Score=23.39 Aligned_cols=46 Identities=24% Similarity=0.499 Sum_probs=20.8
Q ss_pred CCCCcccCC--CCCCCCCHHHHHHHhhhhccC----CCCceecCccccchhh
Q 028603 42 DVRPDFPCP--YCYEDFDIASLCSHLEDEHSC----ESKVTVCPICSVKVAR 87 (206)
Q Consensus 42 d~r~~F~CP--fC~e~fD~~~L~~H~~eeH~~----e~k~vVCPICa~~vs~ 87 (206)
+..+...|+ -|+.-|=..=|.+........ ....+.||.|...++-
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 334567886 888877777777777665443 4555779999987643
No 192
>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=20.77 E-value=60 Score=20.51 Aligned_cols=13 Identities=23% Similarity=0.531 Sum_probs=8.6
Q ss_pred CCCCcccCCCCCC
Q 028603 42 DVRPDFPCPYCYE 54 (206)
Q Consensus 42 d~r~~F~CPfC~e 54 (206)
+......||+||-
T Consensus 13 ~~~~~irC~~CG~ 25 (32)
T PF03604_consen 13 KPGDPIRCPECGH 25 (32)
T ss_dssp STSSTSSBSSSS-
T ss_pred CCCCcEECCcCCC
Confidence 3345678999984
No 193
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.75 E-value=48 Score=26.84 Aligned_cols=14 Identities=43% Similarity=0.866 Sum_probs=11.5
Q ss_pred cccCCCCCCCCCHH
Q 028603 46 DFPCPYCYEDFDIA 59 (206)
Q Consensus 46 ~F~CPfC~e~fD~~ 59 (206)
...||-||+.|+-.
T Consensus 49 ~t~CP~Cg~~~e~~ 62 (115)
T COG1885 49 STSCPKCGEPFESA 62 (115)
T ss_pred cccCCCCCCcccee
Confidence 57899999988754
No 194
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=20.65 E-value=58 Score=29.73 Aligned_cols=29 Identities=28% Similarity=0.552 Sum_probs=21.2
Q ss_pred cccCCCCCCCCCHHHHHHHhhhhccCCCCceecCccccc
Q 028603 46 DFPCPYCYEDFDIASLCSHLEDEHSCESKVTVCPICSVK 84 (206)
Q Consensus 46 ~F~CPfC~e~fD~~~L~~H~~eeH~~e~k~vVCPICa~~ 84 (206)
-..||-|++-+-..+|.. +.-|||-|...
T Consensus 26 ~~~c~~c~~~~~~~~l~~----------~~~vc~~c~~h 54 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELER----------NLEVCPKCDHH 54 (285)
T ss_pred eeECCCCcchhhHHHHHh----------hCCCCCCCCCc
Confidence 457999999776666643 23699999775
No 195
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=20.64 E-value=28 Score=22.37 Aligned_cols=9 Identities=33% Similarity=1.187 Sum_probs=4.9
Q ss_pred CCCCCCCCC
Q 028603 49 CPYCYEDFD 57 (206)
Q Consensus 49 CPfC~e~fD 57 (206)
||-|+..+.
T Consensus 2 CP~C~~~l~ 10 (41)
T PF13453_consen 2 CPRCGTELE 10 (41)
T ss_pred cCCCCcccc
Confidence 566655444
No 196
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=20.56 E-value=33 Score=31.96 Aligned_cols=18 Identities=22% Similarity=0.615 Sum_probs=13.7
Q ss_pred CceecCccccchhhhHhh
Q 028603 74 KVTVCPICSVKVARDMLS 91 (206)
Q Consensus 74 k~vVCPICa~~vs~d~l~ 91 (206)
+..+||||..+|...||.
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 347999999998666653
No 197
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=20.55 E-value=43 Score=29.27 Aligned_cols=19 Identities=32% Similarity=0.695 Sum_probs=16.1
Q ss_pred ecCccccch--hhhHhhhhhc
Q 028603 77 VCPICSVKV--ARDMLSHITL 95 (206)
Q Consensus 77 VCPICa~~v--s~d~l~HL~~ 95 (206)
.|-||...| +.||+.||+.
T Consensus 77 yCdVCdcvvKDSinflDHiNg 97 (193)
T KOG4727|consen 77 YCDVCDCVVKDSINFLDHING 97 (193)
T ss_pred eeeecceeehhhHHHHHHhcc
Confidence 399998887 7799999985
No 198
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=20.37 E-value=48 Score=31.90 Aligned_cols=32 Identities=16% Similarity=0.218 Sum_probs=26.5
Q ss_pred CcccCCCCCC-CCCHHHHHHHhhhhccCCCCce
Q 028603 45 PDFPCPYCYE-DFDIASLCSHLEDEHSCESKVT 76 (206)
Q Consensus 45 ~~F~CPfC~e-~fD~~~L~~H~~eeH~~e~k~v 76 (206)
.+..|=||.. +=+.+.|.+|+.+-|.++-...
T Consensus 278 ~~v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki 310 (423)
T KOG2482|consen 278 LSVVCLFCTNFYENPVFLFEHMKIVHEFDLLKI 310 (423)
T ss_pred cceEEEeeccchhhHHHHHHHHHHHHHhhHHhh
Confidence 3479999999 5559999999999999976543
No 199
>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=20.19 E-value=17 Score=30.26 Aligned_cols=13 Identities=31% Similarity=0.518 Sum_probs=10.3
Q ss_pred CCCcccCCCCCCC
Q 028603 43 VRPDFPCPYCYED 55 (206)
Q Consensus 43 ~r~~F~CPfC~e~ 55 (206)
....|.||||+-+
T Consensus 5 ~~~D~vcPwcylg 17 (209)
T cd03021 5 LYYDVVSPYSYLA 17 (209)
T ss_pred EEEeCCChHHHHH
Confidence 4457999999884
No 200
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.12 E-value=24 Score=32.39 Aligned_cols=42 Identities=31% Similarity=0.665 Sum_probs=28.8
Q ss_pred CcccCCCCCC--CCCHHHHHHHhhhhccC-----CCCceecCccccchh
Q 028603 45 PDFPCPYCYE--DFDIASLCSHLEDEHSC-----ESKVTVCPICSVKVA 86 (206)
Q Consensus 45 ~~F~CPfC~e--~fD~~~L~~H~~eeH~~-----e~k~vVCPICa~~vs 86 (206)
..|.|+.|-+ +-=.-..|-|+---|+. -.+...||+|.+++.
T Consensus 214 ~d~kC~lC~e~~~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~ 262 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY 262 (271)
T ss_pred cccceeeeecccCCcccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence 3799999988 33344556666666653 334566999999863
No 201
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=20.07 E-value=78 Score=24.02 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=23.4
Q ss_pred CcccC----CCCCC-CCCHHHHHHHhhhhcc
Q 028603 45 PDFPC----PYCYE-DFDIASLCSHLEDEHS 70 (206)
Q Consensus 45 ~~F~C----PfC~e-~fD~~~L~~H~~eeH~ 70 (206)
.-|.| +.|+- --+...+..|+..+|.
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 46999 99999 9999999999999983
No 202
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=20.01 E-value=36 Score=25.58 Aligned_cols=9 Identities=44% Similarity=1.375 Sum_probs=8.1
Q ss_pred cccCCCCCC
Q 028603 46 DFPCPYCYE 54 (206)
Q Consensus 46 ~F~CPfC~e 54 (206)
.|.||||..
T Consensus 14 D~~Cp~C~~ 22 (154)
T cd03023 14 DYNCGYCKK 22 (154)
T ss_pred CCCChhHHH
Confidence 689999987
Done!