Query 040287
Match_columns 162
No_of_seqs 260 out of 1648
Neff 9.2
Searched_HMMs 46136
Date Fri Mar 29 06:54:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040287.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040287hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462 C2H2-type Zn-finger pr 99.9 1E-22 2.2E-27 150.5 4.7 109 2-112 134-252 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 4.8E-21 1E-25 141.7 -0.7 91 3-97 166-265 (279)
3 KOG1074 Transcriptional repres 99.6 3.5E-17 7.7E-22 135.8 0.0 48 3-52 358-405 (958)
4 KOG3623 Homeobox transcription 99.5 2.2E-15 4.8E-20 123.8 0.4 71 26-96 892-971 (1007)
5 KOG3576 Ovo and related transc 99.4 1.8E-14 3.8E-19 102.8 -2.8 74 25-98 114-197 (267)
6 KOG1074 Transcriptional repres 99.4 2.1E-13 4.5E-18 113.7 1.6 83 2-101 609-694 (958)
7 KOG3623 Homeobox transcription 99.3 9.5E-13 2.1E-17 108.6 1.6 50 62-111 909-958 (1007)
8 PHA00733 hypothetical protein 99.1 4.5E-11 9.8E-16 81.2 3.7 77 2-100 44-124 (128)
9 KOG3576 Ovo and related transc 99.1 3.7E-11 7.9E-16 86.0 1.1 99 3-103 122-240 (267)
10 PHA02768 hypothetical protein; 99.1 8.7E-11 1.9E-15 67.2 2.4 44 28-92 5-48 (55)
11 KOG3608 Zn finger proteins [Ge 99.0 1.3E-11 2.8E-16 94.7 -2.6 147 2-156 183-370 (467)
12 KOG3608 Zn finger proteins [Ge 98.8 5.4E-10 1.2E-14 85.9 -0.4 96 2-100 267-377 (467)
13 PF13465 zf-H2C2_2: Zinc-finge 98.8 4.7E-09 1E-13 51.4 2.6 26 43-87 1-26 (26)
14 PHA00732 hypothetical protein 98.6 2.5E-08 5.5E-13 62.0 3.0 47 28-99 1-48 (79)
15 PF13465 zf-H2C2_2: Zinc-finge 98.6 6.1E-09 1.3E-13 51.0 -0.9 23 18-40 4-26 (26)
16 PLN03086 PRLI-interacting fact 98.5 1.1E-07 2.4E-12 78.4 4.2 80 27-110 452-548 (567)
17 PHA02768 hypothetical protein; 98.5 8.9E-09 1.9E-13 58.9 -2.0 39 2-44 9-47 (55)
18 PHA00616 hypothetical protein 98.5 4.2E-08 9E-13 53.5 0.4 32 75-106 1-32 (44)
19 COG5189 SFP1 Putative transcri 98.3 3.8E-07 8.3E-12 69.6 3.5 72 24-96 345-419 (423)
20 PHA00616 hypothetical protein 98.3 1.6E-07 3.6E-12 51.2 1.1 29 28-56 1-29 (44)
21 KOG3993 Transcription factor ( 98.3 2E-07 4.3E-12 73.4 1.1 84 18-101 285-382 (500)
22 PF00096 zf-C2H2: Zinc finger, 98.3 3.3E-07 7.3E-12 43.3 1.0 23 76-98 1-23 (23)
23 KOG3993 Transcription factor ( 98.1 2.6E-06 5.7E-11 67.3 3.0 49 2-52 299-380 (500)
24 PF00096 zf-C2H2: Zinc finger, 98.1 2.9E-06 6.3E-11 40.0 1.9 23 29-51 1-23 (23)
25 PF05605 zf-Di19: Drought indu 98.0 7.7E-06 1.7E-10 47.1 3.6 52 28-99 2-53 (54)
26 PLN03086 PRLI-interacting fact 97.9 6.2E-06 1.4E-10 68.3 2.9 86 2-96 457-561 (567)
27 PF13912 zf-C2H2_6: C2H2-type 97.9 6.7E-06 1.4E-10 40.3 1.6 26 75-100 1-26 (27)
28 PHA00733 hypothetical protein 97.9 4.7E-06 1E-10 56.6 0.9 47 2-52 77-123 (128)
29 PF13894 zf-C2H2_4: C2H2-type 97.8 8E-06 1.7E-10 38.5 1.2 23 76-98 1-23 (24)
30 PF13894 zf-C2H2_4: C2H2-type 97.7 3.6E-05 7.8E-10 36.2 2.4 23 29-51 1-23 (24)
31 PF13912 zf-C2H2_6: C2H2-type 97.7 2.6E-05 5.7E-10 38.1 1.6 25 28-52 1-25 (27)
32 PF12756 zf-C2H2_2: C2H2 type 97.7 2.1E-05 4.6E-10 50.5 1.6 69 30-99 1-74 (100)
33 PF09237 GAGA: GAGA factor; I 97.6 3.8E-05 8.1E-10 43.0 2.0 33 71-103 20-52 (54)
34 smart00355 ZnF_C2H2 zinc finge 97.4 5.6E-05 1.2E-09 36.1 1.0 24 76-99 1-24 (26)
35 PRK04860 hypothetical protein; 97.2 0.00035 7.5E-09 49.3 2.9 40 27-89 118-157 (160)
36 smart00355 ZnF_C2H2 zinc finge 97.2 0.00032 6.9E-09 33.3 1.9 24 29-52 1-24 (26)
37 PF09237 GAGA: GAGA factor; I 97.1 0.0008 1.7E-08 37.7 3.0 34 23-56 19-52 (54)
38 PF12874 zf-met: Zinc-finger o 97.0 0.00034 7.4E-09 33.4 1.2 23 76-98 1-23 (25)
39 KOG1146 Homeobox protein [Gene 96.9 0.00065 1.4E-08 60.7 2.4 92 3-97 441-540 (1406)
40 PHA00732 hypothetical protein 96.8 0.00063 1.4E-08 42.3 1.5 26 75-100 1-27 (79)
41 PF12874 zf-met: Zinc-finger o 96.8 0.00077 1.7E-08 32.1 1.4 23 29-51 1-23 (25)
42 PF12171 zf-C2H2_jaz: Zinc-fin 96.7 0.00083 1.8E-08 32.8 1.2 23 76-98 2-24 (27)
43 PF13909 zf-H2C2_5: C2H2-type 96.6 0.00089 1.9E-08 31.6 0.9 23 76-99 1-23 (24)
44 PF13909 zf-H2C2_5: C2H2-type 96.2 0.0036 7.8E-08 29.5 1.7 23 29-52 1-23 (24)
45 COG5048 FOG: Zn-finger [Genera 96.0 0.0056 1.2E-07 48.7 2.8 55 2-58 293-353 (467)
46 PF13913 zf-C2HC_2: zinc-finge 95.9 0.004 8.7E-08 29.8 1.0 21 76-97 3-23 (25)
47 PF12171 zf-C2H2_jaz: Zinc-fin 95.8 0.0027 5.9E-08 30.9 0.2 22 29-50 2-23 (27)
48 PF12756 zf-C2H2_2: C2H2 type 95.1 0.02 4.4E-07 36.3 2.6 25 28-52 50-74 (100)
49 COG5048 FOG: Zn-finger [Genera 94.7 0.011 2.5E-07 46.9 0.8 61 27-106 288-354 (467)
50 smart00451 ZnF_U1 U1-like zinc 94.3 0.04 8.7E-07 28.2 2.0 23 28-50 3-25 (35)
51 smart00451 ZnF_U1 U1-like zinc 94.3 0.028 6E-07 28.8 1.3 23 75-97 3-25 (35)
52 cd00350 rubredoxin_like Rubred 93.2 0.077 1.7E-06 27.1 1.9 11 29-39 2-12 (33)
53 COG5189 SFP1 Putative transcri 93.2 0.085 1.8E-06 41.0 2.9 60 72-148 346-408 (423)
54 COG1592 Rubrerythrin [Energy p 91.6 0.13 2.9E-06 36.4 2.0 24 27-82 133-156 (166)
55 cd00729 rubredoxin_SM Rubredox 91.4 0.18 3.8E-06 26.0 1.9 12 28-39 2-13 (34)
56 KOG2893 Zn finger protein [Gen 91.2 0.091 2E-06 39.2 0.9 49 27-99 10-59 (341)
57 PF09986 DUF2225: Uncharacteri 90.6 0.091 2E-06 38.9 0.4 54 26-88 3-61 (214)
58 PRK04860 hypothetical protein; 90.4 0.15 3.2E-06 36.0 1.3 34 74-111 118-151 (160)
59 KOG1146 Homeobox protein [Gene 89.8 0.23 4.9E-06 45.3 2.3 69 26-97 1282-1350(1406)
60 PF05605 zf-Di19: Drought indu 88.0 0.3 6.5E-06 27.7 1.3 26 75-101 2-28 (54)
61 COG4049 Uncharacterized protei 87.8 0.21 4.7E-06 28.5 0.5 27 71-97 13-39 (65)
62 PRK00398 rpoP DNA-directed RNA 87.5 0.48 1E-05 25.9 1.8 14 27-40 2-15 (46)
63 smart00614 ZnF_BED BED zinc fi 86.2 0.47 1E-05 26.5 1.4 25 75-99 18-48 (50)
64 COG4049 Uncharacterized protei 84.6 0.56 1.2E-05 26.8 1.1 31 21-51 10-40 (65)
65 PF09538 FYDLN_acid: Protein o 84.5 0.64 1.4E-05 30.6 1.6 16 73-88 24-39 (108)
66 PF02892 zf-BED: BED zinc fing 84.0 0.8 1.7E-05 24.7 1.6 25 72-96 13-41 (45)
67 TIGR02098 MJ0042_CXXC MJ0042 f 80.9 1.1 2.4E-05 23.3 1.4 35 28-86 2-36 (38)
68 COG1997 RPL43A Ribosomal prote 80.0 0.95 2.1E-05 28.4 1.0 19 72-90 50-68 (89)
69 smart00531 TFIIE Transcription 80.0 2 4.4E-05 29.7 2.8 40 24-86 95-134 (147)
70 PF09723 Zn-ribbon_8: Zinc rib 79.4 0.6 1.3E-05 25.1 0.0 13 28-40 5-17 (42)
71 COG1996 RPC10 DNA-directed RNA 78.5 1.9 4E-05 24.1 1.8 13 26-38 4-16 (49)
72 KOG2186 Cell growth-regulating 78.1 1.6 3.5E-05 32.9 1.9 49 28-98 3-51 (276)
73 TIGR02605 CxxC_CxxC_SSSS putat 76.8 0.93 2E-05 25.3 0.3 13 28-40 5-17 (52)
74 KOG4124 Putative transcription 76.4 0.94 2E-05 35.8 0.3 69 26-94 347-417 (442)
75 PRK06266 transcription initiat 75.6 1.9 4.1E-05 31.0 1.7 34 25-86 114-147 (178)
76 TIGR00373 conserved hypothetic 74.9 2 4.2E-05 30.3 1.6 35 24-86 105-139 (158)
77 TIGR02300 FYDLN_acid conserved 74.0 2.4 5.1E-05 28.7 1.7 20 73-92 24-43 (129)
78 PRK00464 nrdR transcriptional 74.0 0.69 1.5E-05 32.4 -0.9 21 74-94 27-47 (154)
79 PF05443 ROS_MUCR: ROS/MUCR tr 73.9 2.5 5.3E-05 28.9 1.8 27 25-54 69-95 (132)
80 PF13719 zinc_ribbon_5: zinc-r 73.9 2.6 5.6E-05 21.9 1.5 34 29-86 3-36 (37)
81 smart00659 RPOLCX RNA polymera 72.9 3.5 7.5E-05 22.5 1.9 13 28-40 2-14 (44)
82 smart00734 ZnF_Rad18 Rad18-lik 71.2 2.6 5.6E-05 20.1 1.0 20 76-96 2-21 (26)
83 PF13717 zinc_ribbon_4: zinc-r 70.7 3.2 6.8E-05 21.5 1.4 34 29-86 3-36 (36)
84 PF12013 DUF3505: Protein of u 70.3 2.5 5.5E-05 27.5 1.2 72 25-100 8-109 (109)
85 PF05443 ROS_MUCR: ROS/MUCR tr 69.9 1.9 4.1E-05 29.5 0.5 28 73-103 70-97 (132)
86 PF12013 DUF3505: Protein of u 68.2 4.9 0.00011 26.2 2.3 26 28-53 80-109 (109)
87 TIGR00100 hypA hydrogenase nic 67.2 4.9 0.00011 26.6 2.1 35 5-40 48-82 (115)
88 PRK00564 hypA hydrogenase nick 67.2 5.1 0.00011 26.6 2.2 34 7-40 50-83 (117)
89 PF04959 ARS2: Arsenite-resist 66.7 6 0.00013 29.3 2.7 29 24-52 73-101 (214)
90 PTZ00255 60S ribosomal protein 66.5 2.7 5.9E-05 26.7 0.7 19 72-90 51-69 (90)
91 PF08790 zf-LYAR: LYAR-type C2 66.3 3.3 7.1E-05 20.3 0.8 20 76-96 1-20 (28)
92 PRK12380 hydrogenase nickel in 65.9 5.4 0.00012 26.4 2.1 33 7-40 50-82 (113)
93 PF01780 Ribosomal_L37ae: Ribo 65.6 2.3 5.1E-05 26.9 0.3 16 73-88 51-66 (90)
94 COG2888 Predicted Zn-ribbon RN 65.3 8.8 0.00019 22.3 2.6 10 74-83 49-58 (61)
95 COG4957 Predicted transcriptio 65.0 3.2 6.9E-05 28.3 0.8 25 76-103 77-101 (148)
96 PRK14890 putative Zn-ribbon RN 64.4 4.9 0.00011 23.3 1.4 10 74-83 47-56 (59)
97 PF10571 UPF0547: Uncharacteri 62.7 3.8 8.2E-05 19.6 0.7 11 76-86 15-25 (26)
98 KOG2231 Predicted E3 ubiquitin 62.3 7.3 0.00016 33.7 2.7 21 77-97 184-204 (669)
99 KOG4167 Predicted DNA-binding 62.2 1.6 3.6E-05 37.7 -1.1 26 27-52 791-816 (907)
100 PRK03824 hypA hydrogenase nick 61.3 6.9 0.00015 26.7 2.0 22 20-41 62-83 (135)
101 TIGR00280 L37a ribosomal prote 61.3 3.4 7.4E-05 26.3 0.4 19 72-90 50-68 (91)
102 COG3357 Predicted transcriptio 61.0 4.7 0.0001 25.5 1.0 14 27-40 57-70 (97)
103 PF07754 DUF1610: Domain of un 60.4 4.6 9.9E-05 19.0 0.7 10 74-83 15-24 (24)
104 PF03604 DNA_RNApol_7kD: DNA d 60.3 7.4 0.00016 19.6 1.5 11 75-85 17-27 (32)
105 PRK03681 hypA hydrogenase nick 59.2 8.6 0.00019 25.5 2.1 35 4-39 47-81 (114)
106 COG5236 Uncharacterized conser 58.6 8.3 0.00018 30.7 2.2 70 28-97 151-242 (493)
107 PF09986 DUF2225: Uncharacteri 58.4 3.7 8.1E-05 30.3 0.3 25 73-97 3-27 (214)
108 PF04959 ARS2: Arsenite-resist 58.0 3.9 8.5E-05 30.3 0.4 30 72-101 74-103 (214)
109 smart00834 CxxC_CXXC_SSSS Puta 57.2 5.6 0.00012 20.7 0.8 15 75-89 5-19 (41)
110 KOG4173 Alpha-SNAP protein [In 56.9 2.7 5.9E-05 30.8 -0.6 60 29-98 107-170 (253)
111 COG4530 Uncharacterized protei 56.8 5.7 0.00012 26.1 0.9 16 72-87 23-38 (129)
112 cd00924 Cyt_c_Oxidase_Vb Cytoc 56.0 5.5 0.00012 25.7 0.8 22 18-40 70-91 (97)
113 PRK03976 rpl37ae 50S ribosomal 55.6 4.5 9.7E-05 25.7 0.3 18 72-89 51-68 (90)
114 PF01155 HypA: Hydrogenase exp 55.3 3.9 8.5E-05 27.0 -0.0 35 6-41 49-83 (113)
115 PF05290 Baculo_IE-1: Baculovi 54.6 12 0.00027 25.5 2.3 56 22-90 74-136 (140)
116 PRK09678 DNA-binding transcrip 54.1 4.2 9.1E-05 24.7 -0.0 20 72-91 24-45 (72)
117 KOG2785 C2H2-type Zn-finger pr 53.9 3.8 8.2E-05 32.8 -0.3 70 28-97 3-90 (390)
118 PHA00626 hypothetical protein 53.0 7.7 0.00017 22.3 0.9 15 74-88 22-36 (59)
119 smart00154 ZnF_AN1 AN1-like Zi 51.9 8.2 0.00018 20.3 0.9 14 75-88 12-25 (39)
120 COG1571 Predicted DNA-binding 51.8 8.9 0.00019 31.3 1.5 19 72-90 364-382 (421)
121 PF09845 DUF2072: Zn-ribbon co 51.7 7.4 0.00016 26.5 0.9 15 75-89 1-15 (131)
122 KOG2593 Transcription initiati 51.1 11 0.00023 30.9 1.8 24 22-45 122-145 (436)
123 PF10276 zf-CHCC: Zinc-finger 50.7 9.5 0.00021 20.3 1.0 13 74-86 28-40 (40)
124 PF01363 FYVE: FYVE zinc finge 50.6 10 0.00023 22.2 1.4 15 73-87 23-37 (69)
125 KOG2893 Zn finger protein [Gen 50.4 3.6 7.8E-05 31.0 -0.9 30 22-51 28-58 (341)
126 COG3091 SprT Zn-dependent meta 49.6 9.7 0.00021 26.6 1.2 36 25-84 114-149 (156)
127 PF13878 zf-C2H2_3: zinc-finge 48.9 18 0.00039 19.2 1.9 24 29-52 14-39 (41)
128 KOG2071 mRNA cleavage and poly 48.2 9.6 0.00021 32.4 1.2 29 73-101 416-444 (579)
129 PF15269 zf-C2H2_7: Zinc-finge 47.5 9.8 0.00021 20.8 0.8 23 75-97 20-42 (54)
130 COG1198 PriA Primosomal protei 47.5 15 0.00032 32.4 2.2 19 66-84 466-484 (730)
131 PF01428 zf-AN1: AN1-like Zinc 47.1 8.6 0.00019 20.6 0.5 15 74-88 12-26 (43)
132 cd00065 FYVE FYVE domain; Zinc 47.1 15 0.00032 20.6 1.6 14 74-87 17-30 (57)
133 KOG2785 C2H2-type Zn-finger pr 46.8 21 0.00045 28.8 2.8 70 27-97 165-242 (390)
134 PRK12496 hypothetical protein; 46.4 17 0.00037 25.7 2.1 12 28-39 127-138 (164)
135 KOG2636 Splicing factor 3a, su 46.1 12 0.00025 30.9 1.3 29 68-96 394-423 (497)
136 PF14446 Prok-RING_1: Prokaryo 44.2 19 0.00042 20.5 1.7 12 29-40 6-17 (54)
137 KOG0717 Molecular chaperone (D 43.3 16 0.00034 30.3 1.7 21 29-49 293-313 (508)
138 KOG2482 Predicted C2H2-type Zn 43.1 13 0.00027 29.6 1.1 29 75-103 195-225 (423)
139 PF04423 Rad50_zn_hook: Rad50 43.0 11 0.00023 21.2 0.5 12 77-88 22-33 (54)
140 COG2331 Uncharacterized protei 42.9 5.7 0.00012 24.3 -0.6 12 28-39 12-23 (82)
141 PF01927 Mut7-C: Mut7-C RNAse 42.6 17 0.00037 25.0 1.6 22 73-94 122-143 (147)
142 PRK14873 primosome assembly pr 41.8 23 0.0005 30.9 2.6 11 74-84 421-431 (665)
143 COG5236 Uncharacterized conser 40.2 13 0.00029 29.6 0.8 84 11-97 201-303 (493)
144 COG1773 Rubredoxin [Energy pro 39.2 16 0.00035 20.9 0.8 12 75-86 3-14 (55)
145 PF02176 zf-TRAF: TRAF-type zi 39.0 34 0.00073 19.2 2.3 42 26-87 7-54 (60)
146 TIGR00622 ssl1 transcription f 38.8 33 0.00072 22.7 2.4 25 27-51 80-104 (112)
147 TIGR00595 priA primosomal prot 38.7 25 0.00054 29.5 2.2 13 72-84 250-262 (505)
148 PLN02294 cytochrome c oxidase 38.6 15 0.00033 26.2 0.8 22 18-40 132-153 (174)
149 COG3364 Zn-ribbon containing p 38.5 17 0.00037 23.6 1.0 16 75-90 2-17 (112)
150 KOG0717 Molecular chaperone (D 38.0 15 0.00032 30.5 0.8 22 76-97 293-314 (508)
151 smart00661 RPOL9 RNA polymeras 37.9 29 0.00063 18.9 1.8 14 27-40 19-32 (52)
152 smart00064 FYVE Protein presen 37.1 24 0.00052 20.6 1.5 12 28-39 10-21 (68)
153 KOG2482 Predicted C2H2-type Zn 36.9 22 0.00047 28.4 1.5 23 28-50 195-217 (423)
154 KOG2636 Splicing factor 3a, su 36.7 25 0.00055 29.0 1.9 28 22-49 395-423 (497)
155 KOG4167 Predicted DNA-binding 36.7 54 0.0012 29.0 3.9 79 4-101 294-374 (907)
156 PF10013 DUF2256: Uncharacteri 36.7 18 0.00038 19.5 0.7 15 77-91 10-24 (42)
157 KOG3408 U1-like Zn-finger-cont 36.6 25 0.00054 23.6 1.5 24 27-50 56-79 (129)
158 PF13451 zf-trcl: Probable zin 36.3 18 0.00039 20.2 0.7 18 73-90 2-19 (49)
159 PF14353 CpXC: CpXC protein 35.0 14 0.0003 24.7 0.2 23 75-97 38-60 (128)
160 COG4391 Uncharacterized protei 34.0 18 0.0004 21.1 0.5 19 19-37 15-33 (62)
161 KOG3408 U1-like Zn-finger-cont 32.8 21 0.00047 23.9 0.8 26 72-97 54-79 (129)
162 PLN02748 tRNA dimethylallyltra 32.3 31 0.00068 28.8 1.8 24 27-50 417-441 (468)
163 PF07649 C1_3: C1-like domain; 32.2 29 0.00062 16.8 1.0 12 74-85 14-25 (30)
164 PF07295 DUF1451: Protein of u 32.1 27 0.00059 24.3 1.3 17 21-37 101-121 (146)
165 PF08209 Sgf11: Sgf11 (transcr 32.1 37 0.0008 17.2 1.4 21 75-96 4-24 (33)
166 COG5188 PRP9 Splicing factor 3 31.6 25 0.00054 28.1 1.1 28 69-96 368-396 (470)
167 PF11238 DUF3039: Protein of u 30.8 11 0.00025 21.7 -0.6 26 2-38 29-54 (58)
168 PRK04351 hypothetical protein; 30.5 34 0.00073 23.8 1.5 17 72-88 129-145 (149)
169 PF07975 C1_4: TFIIH C1-like d 30.4 25 0.00055 19.8 0.7 26 74-99 20-45 (51)
170 PF06397 Desulfoferrod_N: Desu 30.3 27 0.00058 18.1 0.7 13 26-38 4-16 (36)
171 PRK00762 hypA hydrogenase nick 30.2 30 0.00064 23.2 1.2 23 18-41 60-82 (124)
172 PF04780 DUF629: Protein of un 30.1 27 0.00058 29.1 1.1 30 73-102 55-85 (466)
173 PF11931 DUF3449: Domain of un 30.0 17 0.00037 26.5 0.0 27 70-96 96-123 (196)
174 COG3677 Transposase and inacti 29.9 26 0.00055 23.8 0.8 17 72-88 50-66 (129)
175 TIGR00416 sms DNA repair prote 28.9 39 0.00084 28.0 1.8 13 27-39 6-18 (454)
176 cd00730 rubredoxin Rubredoxin; 28.9 22 0.00047 19.9 0.3 12 29-40 2-13 (50)
177 KOG2071 mRNA cleavage and poly 28.9 36 0.00078 29.1 1.6 27 25-51 415-441 (579)
178 PF09416 UPF1_Zn_bind: RNA hel 28.7 21 0.00045 25.0 0.2 21 3-23 19-39 (152)
179 KOG2231 Predicted E3 ubiquitin 28.1 40 0.00086 29.4 1.8 24 29-52 183-206 (669)
180 PTZ00448 hypothetical protein; 28.0 30 0.00065 27.8 1.0 23 75-97 314-336 (373)
181 smart00731 SprT SprT homologue 27.8 37 0.00081 23.3 1.4 13 74-86 132-144 (146)
182 PF00301 Rubredoxin: Rubredoxi 27.8 30 0.00066 19.0 0.7 14 28-41 1-14 (47)
183 PRK06260 threonine synthase; V 27.8 45 0.00098 26.9 2.1 11 29-39 4-14 (397)
184 PRK11823 DNA repair protein Ra 27.5 46 0.001 27.5 2.1 14 26-39 5-18 (446)
185 PRK05580 primosome assembly pr 26.7 50 0.0011 28.9 2.2 13 72-84 418-430 (679)
186 KOG3362 Predicted BBOX Zn-fing 26.7 27 0.00058 24.2 0.4 24 73-96 127-150 (156)
187 PF10263 SprT-like: SprT-like 26.0 36 0.00079 23.3 1.1 13 74-86 142-154 (157)
188 PF01215 COX5B: Cytochrome c o 25.9 23 0.00051 24.3 0.1 22 18-40 103-124 (136)
189 PLN02748 tRNA dimethylallyltra 24.1 43 0.00093 28.0 1.3 26 73-98 416-442 (468)
190 COG4338 Uncharacterized protei 23.8 25 0.00054 19.5 -0.1 15 77-91 14-28 (54)
191 PF08274 PhnA_Zn_Ribbon: PhnA 23.8 48 0.001 16.4 0.9 12 73-84 17-28 (30)
192 KOG2807 RNA polymerase II tran 23.5 1.2E+02 0.0027 24.1 3.6 72 27-98 289-368 (378)
193 PF01286 XPA_N: XPA protein N- 23.2 42 0.00091 17.2 0.7 14 76-89 4-17 (34)
194 PF02748 PyrI_C: Aspartate car 23.1 45 0.00096 18.8 0.9 19 22-40 29-47 (52)
195 TIGR01206 lysW lysine biosynth 22.9 38 0.00083 19.3 0.6 13 76-88 3-15 (54)
196 COG1655 Uncharacterized protei 22.1 31 0.00068 25.9 0.1 27 73-99 17-43 (267)
197 KOG4602 Nanos and related prot 22.1 46 0.00099 25.5 1.0 13 73-85 266-278 (318)
198 KOG0402 60S ribosomal protein 21.7 35 0.00076 21.3 0.3 16 73-88 52-67 (92)
199 PF12230 PRP21_like_P: Pre-mRN 21.4 31 0.00068 25.6 0.0 31 73-104 166-196 (229)
200 PF05191 ADK_lid: Adenylate ki 21.2 49 0.0011 17.0 0.7 11 76-86 2-12 (36)
201 PTZ00448 hypothetical protein; 21.2 67 0.0014 25.9 1.8 23 28-50 314-336 (373)
202 PTZ00043 cytochrome c oxidase 21.0 42 0.0009 25.2 0.6 20 20-40 174-193 (268)
203 PF13824 zf-Mss51: Zinc-finger 20.6 58 0.0013 18.7 1.0 15 72-86 11-25 (55)
204 TIGR00244 transcriptional regu 20.5 43 0.00094 23.3 0.6 19 74-92 27-45 (147)
205 COG1675 TFA1 Transcription ini 20.5 57 0.0012 23.5 1.2 17 25-41 110-126 (176)
206 PF14787 zf-CCHC_5: GAG-polypr 20.5 54 0.0012 17.0 0.8 16 76-91 3-18 (36)
207 PF01844 HNH: HNH endonuclease 20.4 30 0.00065 18.2 -0.2 14 78-91 1-14 (47)
208 cd01121 Sms Sms (bacterial rad 20.3 61 0.0013 26.2 1.4 11 29-39 1-11 (372)
209 PF10537 WAC_Acf1_DNA_bd: ATP- 20.2 1.8E+02 0.004 18.8 3.4 38 27-84 2-39 (102)
210 PF06220 zf-U1: U1 zinc finger 20.1 67 0.0015 16.7 1.1 22 75-96 3-26 (38)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.87 E-value=1e-22 Score=150.50 Aligned_cols=109 Identities=20% Similarity=0.317 Sum_probs=96.4
Q ss_pred cchhhhhcCCCCCCccccccccCC---CceeecCccCCccCChhHHHHHHHhcCC-------CCCCCCCCCCCcCccCCC
Q 040287 2 ANCLMFMSQGGHFDAVNSVDMTAA---GRVFECKTCNRQFPSFQALGGHRASHKK-------PRLTDGTGGGADTQQSPA 71 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~h~~---~k~~~C~~C~k~f~~~~~L~~H~~~h~~-------~~~~~~~~~l~~h~~~h~ 71 (162)
.+|||+.+..++|. +|+.+|-. .+.+.|.+|+|.|.+...|++|+++|+- .+.|...+-|+.|+|+|+
T Consensus 134 ~eCgk~ysT~snLs--rHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHT 211 (279)
T KOG2462|consen 134 PECGKSYSTSSNLS--RHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHT 211 (279)
T ss_pred cccccccccccccc--hhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhccccccc
Confidence 57999999999999 99988863 5779999999999999999999999982 223334457799999999
Q ss_pred CCCceecCCCccccccchhHhhhhccccccccCCCCccccc
Q 040287 72 KPRTHECSVCGLEFAIGQALGGHMRRHRAVALHGNEKVSTL 112 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~ 112 (162)
|||||.|+.|+|+|+.+++|+.||++|.+.+++.|..+...
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKS 252 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhH
Confidence 99999999999999999999999999999999998887653
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.80 E-value=4.8e-21 Score=141.67 Aligned_cols=91 Identities=20% Similarity=0.327 Sum_probs=80.9
Q ss_pred chhhhhcCCCCCCccccccccCCCceeecCccCCccCChhHHHHHHHhcCCCCCCCCC---------CCCCcCccCCCCC
Q 040287 3 NCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGT---------GGGADTQQSPAKP 73 (162)
Q Consensus 3 ~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~---------~~l~~h~~~h~~~ 73 (162)
.|+|.+-.--.|. .|+|+|+ -+++|.+|||.|.+.+-|+.|+|+|+|||||.|. ++|+.|+++|.+.
T Consensus 166 ~C~K~YvSmpALk--MHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~ 241 (279)
T KOG2462|consen 166 YCGKVYVSMPALK--MHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDV 241 (279)
T ss_pred CCCceeeehHHHh--hHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCC
Confidence 5888887766777 8999987 6899999999999999999999999999999843 3789999999999
Q ss_pred CceecCCCccccccchhHhhhhcc
Q 040287 74 RTHECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 74 kp~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
|+|+|..|+|+|+..+.|.+|...
T Consensus 242 K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 242 KKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccccCcchhhHHHHHHHHHHhhhh
Confidence 999999999999999999999764
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.63 E-value=3.5e-17 Score=135.77 Aligned_cols=48 Identities=19% Similarity=0.421 Sum_probs=45.2
Q ss_pred chhhhhcCCCCCCccccccccCCCceeecCccCCccCChhHHHHHHHhcC
Q 040287 3 NCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 3 ~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
.|.|.|..++.|. .|.|.|+||+||+|.+||..|.++.+|+.|...|+
T Consensus 358 ~CakvfgS~SaLq--iHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 358 FCAKVFGSDSALQ--IHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred hhHhhcCchhhhh--hhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 6999999999999 99999999999999999999999999999987665
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.51 E-value=2.2e-15 Score=123.77 Aligned_cols=71 Identities=17% Similarity=0.386 Sum_probs=47.8
Q ss_pred CceeecCccCCccCChhHHHHHHHhcCCCCCCCCCC---------CCCcCccCCCCCCceecCCCccccccchhHhhhhc
Q 040287 26 GRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTG---------GGADTQQSPAKPRTHECSVCGLEFAIGQALGGHMR 96 (162)
Q Consensus 26 ~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~---------~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~ 96 (162)
+..|.|+.|+|.|...+.|.+|.--|+|.+||.|.. .|..|+|.|.|||||.|..|+|+|+.++....||.
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 334555555555555555555555555555555321 33445555569999999999999999999999986
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.38 E-value=1.8e-14 Score=102.76 Aligned_cols=74 Identities=22% Similarity=0.389 Sum_probs=52.5
Q ss_pred CCceeecCccCCccCChhHHHHHHHhcCCCCCCC---------CCCCCCcCccCCCCCCceecCCCccccccchhHhhhh
Q 040287 25 AGRVFECKTCNRQFPSFQALGGHRASHKKPRLTD---------GTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGHM 95 (162)
Q Consensus 25 ~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~---------~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~ 95 (162)
+.-.|.|.+|+|.|.....|.+|++-|...+.+- ....|++|+++|+|.+||+|..|+++|.+.-.|..|.
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl 193 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHL 193 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHH
Confidence 3445777777777777777777777666544322 1225667777777899999999999999999999997
Q ss_pred c-cc
Q 040287 96 R-RH 98 (162)
Q Consensus 96 ~-~H 98 (162)
+ +|
T Consensus 194 ~kvh 197 (267)
T KOG3576|consen 194 KKVH 197 (267)
T ss_pred HHHc
Confidence 6 45
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.35 E-value=2.1e-13 Score=113.71 Aligned_cols=83 Identities=25% Similarity=0.434 Sum_probs=76.0
Q ss_pred cchhhhhcCCCCCCccccccccCCCceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecC--
Q 040287 2 ANCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECS-- 79 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~-- 79 (162)
..|.+.+++.+.|. .|.|+|+||+||+|.+||+.|.++.+|+.|+-+|....++ .-++.|+
T Consensus 609 iiC~rVlSC~saLq--mHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~---------------R~q~ScP~~ 671 (958)
T KOG1074|consen 609 IICLRVLSCPSALQ--MHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPA---------------RVQFSCPST 671 (958)
T ss_pred eeeeecccchhhhh--hhhhcccCcCccccccccchhccccchhhcccccccCccc---------------cccccCCch
Confidence 46999999999999 9999999999999999999999999999999999766554 2579999
Q ss_pred -CCccccccchhHhhhhcccccc
Q 040287 80 -VCGLEFAIGQALGGHMRRHRAV 101 (162)
Q Consensus 80 -~C~k~F~~~~~L~~H~~~H~~~ 101 (162)
+|-+.|...-.|..|+++|.+.
T Consensus 672 ~ic~~kftn~V~lpQhIriH~~~ 694 (958)
T KOG1074|consen 672 FICQKKFTNAVTLPQHIRIHLGG 694 (958)
T ss_pred hhhcccccccccccceEEeecCC
Confidence 9999999999999999999844
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.28 E-value=9.5e-13 Score=108.56 Aligned_cols=50 Identities=20% Similarity=0.252 Sum_probs=29.3
Q ss_pred CCCcCccCCCCCCceecCCCccccccchhHhhhhccccccccCCCCcccc
Q 040287 62 GGADTQQSPAKPRTHECSVCGLEFAIGQALGGHMRRHRAVALHGNEKVST 111 (162)
Q Consensus 62 ~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~ 111 (162)
.|.+|.--|+|.+||+|.+|.|+|..+.+|..|+|.|.||+|+.|+.+..
T Consensus 909 SLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClK 958 (1007)
T KOG3623|consen 909 SLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLK 958 (1007)
T ss_pred HHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhh
Confidence 34555555666666666666666666666666666666666655555543
No 8
>PHA00733 hypothetical protein
Probab=99.13 E-value=4.5e-11 Score=81.18 Aligned_cols=77 Identities=21% Similarity=0.311 Sum_probs=61.3
Q ss_pred cchhhhhcCCCCCCcc----ccccccCCCceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCcee
Q 040287 2 ANCLMFMSQGGHFDAV----NSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHE 77 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~----~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~ 77 (162)
+.|.+.|.+...|.-. .|+..+ +++||.|+.|++.|.+...|..|++.|. .+|.
T Consensus 44 ~~~~~~~~~~~~l~~~~~l~~~~~~~-~~kPy~C~~Cgk~Fss~s~L~~H~r~h~---------------------~~~~ 101 (128)
T PHA00733 44 AVVKTLIYNPQLLDESSYLYKLLTSK-AVSPYVCPLCLMPFSSSVSLKQHIRYTE---------------------HSKV 101 (128)
T ss_pred HHHhhhccChhhhcchHHHHhhcccC-CCCCccCCCCCCcCCCHHHHHHHHhcCC---------------------cCcc
Confidence 3577777777666633 343444 4789999999999999999999988652 3689
Q ss_pred cCCCccccccchhHhhhhccccc
Q 040287 78 CSVCGLEFAIGQALGGHMRRHRA 100 (162)
Q Consensus 78 C~~C~k~F~~~~~L~~H~~~H~~ 100 (162)
|..|++.|.....|.+|+...++
T Consensus 102 C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 102 CPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCCccCCHHHHHHHHHHhcC
Confidence 99999999999999999887554
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.07 E-value=3.7e-11 Score=85.95 Aligned_cols=99 Identities=13% Similarity=0.187 Sum_probs=82.5
Q ss_pred chhhhhcCCCCCCccccccccCCCceeecCccCCccCChhHHHHHHHhcCCCCCCCCC---------CCCCcCcc-CC--
Q 040287 3 NCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGT---------GGGADTQQ-SP-- 70 (162)
Q Consensus 3 ~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~---------~~l~~h~~-~h-- 70 (162)
.|||.|.-++.|. +|++-|++-|.|.|..|||.|...-+|++|+|+|+|.+||+|. |.|..|.+ +|
T Consensus 122 vCgK~F~lQRmln--rh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv 199 (267)
T KOG3576|consen 122 VCGKKFGLQRMLN--RHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGV 199 (267)
T ss_pred hhhhhhhHHHHHH--HHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCc
Confidence 5999999999999 9999999999999999999999999999999999999999843 34544543 22
Q ss_pred --------CCCCceecCCCccccccchhHhhhhcccccccc
Q 040287 71 --------AKPRTHECSVCGLEFAIGQALGGHMRRHRAVAL 103 (162)
Q Consensus 71 --------~~~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~ 103 (162)
..+|-|.|+.||.+-.....+..|.+.|....+
T Consensus 200 ~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Sp 240 (267)
T KOG3576|consen 200 QHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSP 240 (267)
T ss_pred hHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCH
Confidence 236789999999999999999999988765433
No 10
>PHA02768 hypothetical protein; Provisional
Probab=99.06 E-value=8.7e-11 Score=67.17 Aligned_cols=44 Identities=16% Similarity=0.199 Sum_probs=39.8
Q ss_pred eeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccchhHh
Q 040287 28 VFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQALG 92 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~ 92 (162)
-|.|++||+.|...++|..|+++|+ ++|+|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~---------------------k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN---------------------TNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC---------------------CcccCCcccceecccceeE
Confidence 4899999999999999999999994 5899999999999888764
No 11
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.03 E-value=1.3e-11 Score=94.66 Aligned_cols=147 Identities=15% Similarity=0.185 Sum_probs=93.0
Q ss_pred cchhhhhcCCCCCCccccccccCCCceeecCccCCccCChhHHHHHHHhcC--CCCCCC---------------------
Q 040287 2 ANCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHK--KPRLTD--------------------- 58 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~--~~~~~~--------------------- 58 (162)
|.|.+.|.++++|. +|+|.|++||...|+.||.-|.++..|-.|.+..+ ...+|.
T Consensus 183 ~~Ct~~~~~k~~Lr--eH~r~Hs~eKvvACp~Cg~~F~~~tkl~DH~rRqt~l~~n~fqC~~C~KrFaTeklL~~Hv~rH 260 (467)
T KOG3608|consen 183 AMCTKHMGNKYRLR--EHIRTHSNEKVVACPHCGELFRTKTKLFDHLRRQTELNTNSFQCAQCFKRFATEKLLKSHVVRH 260 (467)
T ss_pred hhhhhhhccHHHHH--HHHHhcCCCeEEecchHHHHhccccHHHHHHHhhhhhcCCchHHHHHHHHHhHHHHHHHHHHHh
Confidence 56777777777777 88888888877777777777777777776654332 122221
Q ss_pred -----C---------CCCCCcCcc-CCCCCCceecCCCccccccchhHhhhhccccccccCCCCcccccccCCCCchhh-
Q 040287 59 -----G---------TGGGADTQQ-SPAKPRTHECSVCGLEFAIGQALGGHMRRHRAVALHGNEKVSTLTLSDTAPLVK- 122 (162)
Q Consensus 59 -----~---------~~~l~~h~~-~h~~~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~~~~~~~~~~~~- 122 (162)
| .+.|..|++ .|...|||+|..|++.|.+.+.|.+|..+|+ +....++-..-.- ++..
T Consensus 261 vn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~-----s~r~~ 334 (467)
T KOG3608|consen 261 VNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHY-----SVRTY 334 (467)
T ss_pred hhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcH-----HHHHH
Confidence 1 114567877 5888999999999999999999999999998 4443333211000 0000
Q ss_pred hcCCCccccc--CCCCCCCCCchhhhhccCCCCCCC
Q 040287 123 KANSRRVLCL--DLNLTPYENDLECHRLGSNKAAAP 156 (162)
Q Consensus 123 ~~~~~~~~~~--d~nl~p~~~d~~~~~~~~~~~~~~ 156 (162)
.+-....... .-|.++|.+.++-.-|++...+.+
T Consensus 335 ~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~ 370 (467)
T KOG3608|consen 335 TQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSA 370 (467)
T ss_pred HHHHHHHHHhccCCCCCceeeecchhhhccchhHHH
Confidence 0111111122 356778999888866766555443
No 12
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.82 E-value=5.4e-10 Score=85.90 Aligned_cols=96 Identities=17% Similarity=0.309 Sum_probs=75.1
Q ss_pred cchhhhhcCCCCCCccccccc-cCCCceeecCccCCccCChhHHHHHHHhcCCCCCCCCC---C--------CCCcCcc-
Q 040287 2 ANCLMFMSQGGHFDAVNSVDM-TAAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGT---G--------GGADTQQ- 68 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~-h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~---~--------~l~~h~~- 68 (162)
+.|.+..+..+.|. .|+|. |+..|||+|+.|++.|.+.+.|.+|..+|+ +..|.|+ | .+.+|.+
T Consensus 267 plCdmtc~~~ssL~--~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~H~~e 343 (467)
T KOG3608|consen 267 PLCDMTCSSASSLT--THIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRRHFLE 343 (467)
T ss_pred cccccCCCChHHHH--HHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHHHHHH
Confidence 46777777777777 88876 888999999999999999999999999998 4445532 2 3456665
Q ss_pred CCCC--CCceecCCCccccccchhHhhhhccccc
Q 040287 69 SPAK--PRTHECSVCGLEFAIGQALGGHMRRHRA 100 (162)
Q Consensus 69 ~h~~--~kp~~C~~C~k~F~~~~~L~~H~~~H~~ 100 (162)
+|.| +.+|.|..|++.|.+..+|..|++..++
T Consensus 344 vhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 344 VHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred hccCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 4444 5679999999999999999999765333
No 13
>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=98.79 E-value=4.7e-09 Score=51.42 Aligned_cols=26 Identities=27% Similarity=0.584 Sum_probs=21.8
Q ss_pred HHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCcccccc
Q 040287 43 ALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAI 87 (162)
Q Consensus 43 ~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~ 87 (162)
+|.+|+++|+ |++||.|+.|+++|.+
T Consensus 1 ~l~~H~~~H~-------------------~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHT-------------------GEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHS-------------------SSSSEEESSSSEEESS
T ss_pred CHHHHhhhcC-------------------CCCCCCCCCCcCeeCc
Confidence 4677777776 8999999999999974
No 14
>PHA00732 hypothetical protein
Probab=98.63 E-value=2.5e-08 Score=61.97 Aligned_cols=47 Identities=26% Similarity=0.553 Sum_probs=39.4
Q ss_pred eeecCccCCccCChhHHHHHHHh-cCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccchhHhhhhcccc
Q 040287 28 VFECKTCNRQFPSFQALGGHRAS-HKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGHMRRHR 99 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~-h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~~H~ 99 (162)
||.|+.|++.|.+..+|..|++. |. ++.|+.||++|. .+..|.+++.
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~----------------------~~~C~~CgKsF~---~l~~H~~~~~ 48 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT----------------------LTKCPVCNKSYR---RLNQHFYSQY 48 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC----------------------CCccCCCCCEeC---ChhhhhcccC
Confidence 58999999999999999999984 53 358999999998 5778876553
No 15
>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=98.57 E-value=6.1e-09 Score=51.02 Aligned_cols=23 Identities=13% Similarity=0.582 Sum_probs=21.5
Q ss_pred ccccccCCCceeecCccCCccCC
Q 040287 18 NSVDMTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 18 ~h~~~h~~~k~~~C~~C~k~f~~ 40 (162)
.|+++|++++||.|++|++.|.+
T Consensus 4 ~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 4 RHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHSSSSSEEESSSSEEESS
T ss_pred HHhhhcCCCCCCCCCCCcCeeCc
Confidence 89999999999999999999963
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.50 E-value=1.1e-07 Score=78.45 Aligned_cols=80 Identities=14% Similarity=0.190 Sum_probs=60.0
Q ss_pred ceeecCccCCccCChhHHHHHHHhcCCCCCCCCCC-------CCCcCccCCCCCCceecCCCcccccc----------ch
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTG-------GGADTQQSPAKPRTHECSVCGLEFAI----------GQ 89 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~-------~l~~h~~~h~~~kp~~C~~C~k~F~~----------~~ 89 (162)
+++.|+.|++.|. ...|..|++.|+ +++.|.| .|..|+.+|..++|+.|++|++.|.. ..
T Consensus 452 ~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~CpCg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s 528 (567)
T PLN03086 452 NHVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCPCGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLR 528 (567)
T ss_pred cCccCCCCCCccc-hHHHHHHHHhcC--CCccCCCCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhh
Confidence 3468999999996 678999999875 5555444 34568888889999999999999853 34
Q ss_pred hHhhhhccccccccCCCCccc
Q 040287 90 ALGGHMRRHRAVALHGNEKVS 110 (162)
Q Consensus 90 ~L~~H~~~H~~~~~~~~~~~~ 110 (162)
.|..|...+ |.++..|..+.
T Consensus 529 ~Lt~HE~~C-G~rt~~C~~Cg 548 (567)
T PLN03086 529 GMSEHESIC-GSRTAPCDSCG 548 (567)
T ss_pred hHHHHHHhc-CCcceEccccC
Confidence 788888875 67776665543
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.47 E-value=8.9e-09 Score=58.93 Aligned_cols=39 Identities=8% Similarity=0.044 Sum_probs=35.4
Q ss_pred cchhhhhcCCCCCCccccccccCCCceeecCccCCccCChhHH
Q 040287 2 ANCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSFQAL 44 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~~~L 44 (162)
.+|||.|++...|. .|+++|+ ++|+|..|++.|.+.+.|
T Consensus 9 ~~CGK~Fs~~~~L~--~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 9 PICGEIYIKRKSMI--THLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred chhCCeeccHHHHH--HHHHhcC--CcccCCcccceeccccee
Confidence 47999999999999 9999999 799999999999877654
No 18
>PHA00616 hypothetical protein
Probab=98.45 E-value=4.2e-08 Score=53.55 Aligned_cols=32 Identities=16% Similarity=0.139 Sum_probs=29.2
Q ss_pred ceecCCCccccccchhHhhhhccccccccCCC
Q 040287 75 THECSVCGLEFAIGQALGGHMRRHRAVALHGN 106 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~ 106 (162)
||+|+.||+.|...+.|.+|++.|+++++...
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 69999999999999999999999999987543
No 19
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.35 E-value=3.8e-07 Score=69.56 Aligned_cols=72 Identities=21% Similarity=0.453 Sum_probs=51.1
Q ss_pred CCCceeecCc--cCCccCChhHHHHHHHh-cCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccchhHhhhhc
Q 040287 24 AAGRVFECKT--CNRQFPSFQALGGHRAS-HKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGHMR 96 (162)
Q Consensus 24 ~~~k~~~C~~--C~k~f~~~~~L~~H~~~-h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~ 96 (162)
.++|||+|++ |+|.|+....|+.|+.. |...+..... .-..+.-.-...|||.|++|+|++.....|+-|..
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p-~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENP-SPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhhccccCcccCCCC-CccccccccccCCceeccccchhhccCccceeccc
Confidence 4579999976 99999999999999864 3222221111 11122222346799999999999999999998854
No 20
>PHA00616 hypothetical protein
Probab=98.34 E-value=1.6e-07 Score=51.21 Aligned_cols=29 Identities=21% Similarity=0.370 Sum_probs=25.8
Q ss_pred eeecCccCCccCChhHHHHHHHhcCCCCC
Q 040287 28 VFECKTCNRQFPSFQALGGHRASHKKPRL 56 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~h~~~~~ 56 (162)
||.|..||+.|..++.|..|++.|+++++
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~ 29 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNK 29 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCc
Confidence 68999999999999999999999984443
No 21
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.30 E-value=2e-07 Score=73.44 Aligned_cols=84 Identities=19% Similarity=0.310 Sum_probs=56.3
Q ss_pred ccccccCCCceeecCccCCccCChhHHHHHHHhcCCCCCCC--------CCC----CCCcCccC--CCCCCceecCCCcc
Q 040287 18 NSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTD--------GTG----GGADTQQS--PAKPRTHECSVCGL 83 (162)
Q Consensus 18 ~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~--------~~~----~l~~h~~~--h~~~kp~~C~~C~k 83 (162)
+|.--..-..-|+|.+|+|.|.-..+|..|+|+|.-...-. ... ..+.-.+. -..+..|.|.+|++
T Consensus 285 QHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~K 364 (500)
T KOG3993|consen 285 QHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGK 364 (500)
T ss_pred hccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhh
Confidence 55533333346999999999999999999999995322111 000 00001111 12244799999999
Q ss_pred ccccchhHhhhhcccccc
Q 040287 84 EFAIGQALGGHMRRHRAV 101 (162)
Q Consensus 84 ~F~~~~~L~~H~~~H~~~ 101 (162)
.|++...|++|+.+|...
T Consensus 365 kFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 365 KFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred hhHHHHHHHHhHHhhhcc
Confidence 999999999998887543
No 22
>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=98.26 E-value=3.3e-07 Score=43.33 Aligned_cols=23 Identities=43% Similarity=0.911 Sum_probs=21.6
Q ss_pred eecCCCccccccchhHhhhhccc
Q 040287 76 HECSVCGLEFAIGQALGGHMRRH 98 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~H 98 (162)
|.|+.|+++|.+...|.+|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 78999999999999999999875
No 23
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.07 E-value=2.6e-06 Score=67.27 Aligned_cols=49 Identities=20% Similarity=0.451 Sum_probs=43.0
Q ss_pred cchhhhhcCCCCCCccccccccCC---------------------------------CceeecCccCCccCChhHHHHHH
Q 040287 2 ANCLMFMSQGGHFDAVNSVDMTAA---------------------------------GRVFECKTCNRQFPSFQALGGHR 48 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~h~~---------------------------------~k~~~C~~C~k~f~~~~~L~~H~ 48 (162)
++|+|.|++-.+|. .|.|+|.- +..|.|.+|+|.|.++..|+.|+
T Consensus 299 PEC~KVFsCPANLA--SHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHq 376 (500)
T KOG3993|consen 299 PECDKVFSCPANLA--SHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQ 376 (500)
T ss_pred CcccccccCchhhh--hhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhH
Confidence 58999999999999 99999952 12499999999999999999998
Q ss_pred HhcC
Q 040287 49 ASHK 52 (162)
Q Consensus 49 ~~h~ 52 (162)
.+|.
T Consensus 377 lthq 380 (500)
T KOG3993|consen 377 LTHQ 380 (500)
T ss_pred Hhhh
Confidence 8775
No 24
>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=98.05 E-value=2.9e-06 Score=40.01 Aligned_cols=23 Identities=30% Similarity=0.710 Sum_probs=21.6
Q ss_pred eecCccCCccCChhHHHHHHHhc
Q 040287 29 FECKTCNRQFPSFQALGGHRASH 51 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~h 51 (162)
|+|+.|++.|.....|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 78999999999999999999875
No 25
>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=98.02 E-value=7.7e-06 Score=47.13 Aligned_cols=52 Identities=19% Similarity=0.445 Sum_probs=39.3
Q ss_pred eeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccchhHhhhhcccc
Q 040287 28 VFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGHMRRHR 99 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~~H~ 99 (162)
.|.|+.|++. .....|..|....+.. ..+.+.|++|...+. .+|.+|+..++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~-----------------~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRS-----------------ESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcC-----------------CCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 4899999995 5578899997654321 235799999998655 49999998754
No 26
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.93 E-value=6.2e-06 Score=68.32 Aligned_cols=86 Identities=19% Similarity=0.337 Sum_probs=66.9
Q ss_pred cchhhhhcCCCCCCccccccccCCCceeecCccCCccCChhHHHHHHHhcCCCCCCCCC-C------------------C
Q 040287 2 ANCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGT-G------------------G 62 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~-~------------------~ 62 (162)
..|++.|. ...|. .|++++. +++.|+ ||+.+ ....|..|+.+|...+++.|. | .
T Consensus 457 ~~Cgk~f~-~s~Le--kH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~ 529 (567)
T PLN03086 457 EKCGQAFQ-QGEME--KHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRG 529 (567)
T ss_pred CCCCCccc-hHHHH--HHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhh
Confidence 36999995 56677 9999874 899999 99766 568999999999999987743 2 2
Q ss_pred CCcCccCCCCCCceecCCCccccccchhHhhhhc
Q 040287 63 GADTQQSPAKPRTHECSVCGLEFAIGQALGGHMR 96 (162)
Q Consensus 63 l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~ 96 (162)
|..|.... |.+++.|..||+.|..+ .|..|+-
T Consensus 530 Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~ 561 (567)
T PLN03086 530 MSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQI 561 (567)
T ss_pred HHHHHHhc-CCcceEccccCCeeeeh-hHHHHHH
Confidence 45676665 89999999999998754 4566654
No 27
>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=97.90 E-value=6.7e-06 Score=40.33 Aligned_cols=26 Identities=38% Similarity=0.645 Sum_probs=23.9
Q ss_pred ceecCCCccccccchhHhhhhccccc
Q 040287 75 THECSVCGLEFAIGQALGGHMRRHRA 100 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~H~~ 100 (162)
||.|..|++.|.....|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999998853
No 28
>PHA00733 hypothetical protein
Probab=97.86 E-value=4.7e-06 Score=56.64 Aligned_cols=47 Identities=19% Similarity=0.357 Sum_probs=41.4
Q ss_pred cchhhhhcCCCCCCccccccccCCCceeecCccCCccCChhHHHHHHHhcC
Q 040287 2 ANCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
..||+.|.+...|. .|+++| +.+|.|.+|++.|.....|..|++..+
T Consensus 77 ~~Cgk~Fss~s~L~--~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 77 PLCLMPFSSSVSLK--QHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCCcCCCHHHHH--HHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 36999999999998 998877 457999999999999999999997654
No 29
>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=97.83 E-value=8e-06 Score=38.55 Aligned_cols=23 Identities=39% Similarity=0.859 Sum_probs=19.7
Q ss_pred eecCCCccccccchhHhhhhccc
Q 040287 76 HECSVCGLEFAIGQALGGHMRRH 98 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~H 98 (162)
|.|++|++.|.+...|..|+++|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 78999999999999999999876
No 30
>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=97.70 E-value=3.6e-05 Score=36.20 Aligned_cols=23 Identities=35% Similarity=0.756 Sum_probs=19.7
Q ss_pred eecCccCCccCChhHHHHHHHhc
Q 040287 29 FECKTCNRQFPSFQALGGHRASH 51 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~h 51 (162)
|.|++|++.|.+...|..|++.|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 78999999999999999999876
No 31
>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=97.67 E-value=2.6e-05 Score=38.15 Aligned_cols=25 Identities=44% Similarity=0.869 Sum_probs=23.4
Q ss_pred eeecCccCCccCChhHHHHHHHhcC
Q 040287 28 VFECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
+|.|..|++.|.+...|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 6899999999999999999998875
No 32
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.67 E-value=2.1e-05 Score=50.49 Aligned_cols=69 Identities=22% Similarity=0.386 Sum_probs=22.4
Q ss_pred ecCccCCccCChhHHHHHHHhcCCCCCCC-----CCCCCCcCccCCCCCCceecCCCccccccchhHhhhhcccc
Q 040287 30 ECKTCNRQFPSFQALGGHRASHKKPRLTD-----GTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGHMRRHR 99 (162)
Q Consensus 30 ~C~~C~k~f~~~~~L~~H~~~h~~~~~~~-----~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~~H~ 99 (162)
.|..|+..|.....|..|+...++-..-. ....+..+.+.- ....+.|..|++.|.+...|..||+.+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~-~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKK-VKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp -------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred Cccccccccccccccccccccccccccccccccccccccccccccc-cCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 48899999999999999986544422111 111222222211 1237999999999999999999999753
No 33
>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=97.63 E-value=3.8e-05 Score=42.97 Aligned_cols=33 Identities=15% Similarity=0.340 Sum_probs=24.3
Q ss_pred CCCCceecCCCccccccchhHhhhhcccccccc
Q 040287 71 AKPRTHECSVCGLEFAIGQALGGHMRRHRAVAL 103 (162)
Q Consensus 71 ~~~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~ 103 (162)
..+.|..|++|+..+++..+|++|+.++++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 367899999999999999999999998887776
No 34
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.44 E-value=5.6e-05 Score=36.06 Aligned_cols=24 Identities=42% Similarity=0.711 Sum_probs=22.0
Q ss_pred eecCCCccccccchhHhhhhcccc
Q 040287 76 HECSVCGLEFAIGQALGGHMRRHR 99 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~H~ 99 (162)
|.|..|+++|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 679999999999999999999775
No 35
>PRK04860 hypothetical protein; Provisional
Probab=97.17 E-value=0.00035 Score=49.26 Aligned_cols=40 Identities=18% Similarity=0.424 Sum_probs=33.8
Q ss_pred ceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccch
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQ 89 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~ 89 (162)
-+|.|. |++ ....+.+|.++|+ ++++|.|..|+..|....
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~-------------------g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVR-------------------GEAVYRCRRCGETLVFKG 157 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhc-------------------CCccEECCCCCceeEEec
Confidence 479998 998 5678899999997 788999999999987544
No 36
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.16 E-value=0.00032 Score=33.29 Aligned_cols=24 Identities=33% Similarity=0.693 Sum_probs=21.9
Q ss_pred eecCccCCccCChhHHHHHHHhcC
Q 040287 29 FECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 679999999999999999999774
No 37
>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=97.05 E-value=0.0008 Score=37.70 Aligned_cols=34 Identities=12% Similarity=0.192 Sum_probs=23.7
Q ss_pred cCCCceeecCccCCccCChhHHHHHHHhcCCCCC
Q 040287 23 TAAGRVFECKTCNRQFPSFQALGGHRASHKKPRL 56 (162)
Q Consensus 23 h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~ 56 (162)
+..+.|-.|++|+..+.+..+|++|+..+++.+|
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3457899999999999999999999987765554
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.02 E-value=0.00034 Score=33.39 Aligned_cols=23 Identities=26% Similarity=0.660 Sum_probs=21.3
Q ss_pred eecCCCccccccchhHhhhhccc
Q 040287 76 HECSVCGLEFAIGQALGGHMRRH 98 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~H 98 (162)
|.|..|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999999865
No 39
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.86 E-value=0.00065 Score=60.75 Aligned_cols=92 Identities=14% Similarity=0.289 Sum_probs=63.7
Q ss_pred chhhhhcCCCCCCccccc-cccCCCceeecCccCCccCChhHHHHHHHhcCC-CCCCCCCCCCCcCccCC------CCCC
Q 040287 3 NCLMFMSQGGHFDAVNSV-DMTAAGRVFECKTCNRQFPSFQALGGHRASHKK-PRLTDGTGGGADTQQSP------AKPR 74 (162)
Q Consensus 3 ~C~k~f~~~~~l~~~~h~-~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~-~~~~~~~~~l~~h~~~h------~~~k 74 (162)
-|+..|.+++.+. .|+ ..++..+.|+|..|+..|+....|..|+|+-+- .+.-.|+ ....|.+.. .+-+
T Consensus 441 ~~e~~~~s~r~~~--~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~-~gq~~~~~arg~~~~~~~~ 517 (1406)
T KOG1146|consen 441 KAEPLLESKRSLE--GQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCK-AGQNHPRLARGEVYRCPGK 517 (1406)
T ss_pred chhhhhhhhcccc--cceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhH-hccccccccccccccCCCC
Confidence 3455565555555 443 457777999999999999999999999997332 1110011 112222222 2457
Q ss_pred ceecCCCccccccchhHhhhhcc
Q 040287 75 THECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
||.|..|..++..+.+|.+|+..
T Consensus 518 p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 518 PYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred cccceeeeeeeecchHHHHHHHH
Confidence 99999999999999999999874
No 40
>PHA00732 hypothetical protein
Probab=96.81 E-value=0.00063 Score=42.25 Aligned_cols=26 Identities=35% Similarity=0.634 Sum_probs=23.4
Q ss_pred ceecCCCccccccchhHhhhhcc-ccc
Q 040287 75 THECSVCGLEFAIGQALGGHMRR-HRA 100 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~-H~~ 100 (162)
||.|+.||+.|.+..+|.+|++. |.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~ 27 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL 27 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC
Confidence 68999999999999999999984 664
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.79 E-value=0.00077 Score=32.11 Aligned_cols=23 Identities=39% Similarity=0.716 Sum_probs=21.1
Q ss_pred eecCccCCccCChhHHHHHHHhc
Q 040287 29 FECKTCNRQFPSFQALGGHRASH 51 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~h 51 (162)
|.|.+|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 78999999999999999998764
No 42
>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=96.72 E-value=0.00083 Score=32.77 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=21.1
Q ss_pred eecCCCccccccchhHhhhhccc
Q 040287 76 HECSVCGLEFAIGQALGGHMRRH 98 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~H 98 (162)
|.|..|++.|.+...+..|+++.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 78999999999999999999863
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.63 E-value=0.00089 Score=31.62 Aligned_cols=23 Identities=26% Similarity=0.629 Sum_probs=18.6
Q ss_pred eecCCCccccccchhHhhhhcccc
Q 040287 76 HECSVCGLEFAIGQALGGHMRRHR 99 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~H~ 99 (162)
|.|+.|+.+.. ...|.+|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999999998 889999998864
No 44
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.20 E-value=0.0036 Score=29.46 Aligned_cols=23 Identities=22% Similarity=0.496 Sum_probs=18.5
Q ss_pred eecCccCCccCChhHHHHHHHhcC
Q 040287 29 FECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
|+|+.|+.... ...|..|++.+.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999999998 899999998763
No 45
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=95.98 E-value=0.0056 Score=48.66 Aligned_cols=55 Identities=18% Similarity=0.352 Sum_probs=49.2
Q ss_pred cchhhhhcCCCCCCcccccc--ccCCC--ceeecC--ccCCccCChhHHHHHHHhcCCCCCCC
Q 040287 2 ANCLMFMSQGGHFDAVNSVD--MTAAG--RVFECK--TCNRQFPSFQALGGHRASHKKPRLTD 58 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~--~h~~~--k~~~C~--~C~k~f~~~~~L~~H~~~h~~~~~~~ 58 (162)
+.|.+.|++...|. .|.+ .|+++ +++.|. .|++.|.....+..|...|.+..+..
T Consensus 293 ~~~~~~~s~~~~l~--~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 (467)
T COG5048 293 KQCNISFSRSSPLT--RHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAK 353 (467)
T ss_pred ccccCCcccccccc--ccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccc
Confidence 46888999999999 9999 89999 999999 89999999999999999998766543
No 46
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.89 E-value=0.004 Score=29.82 Aligned_cols=21 Identities=29% Similarity=0.618 Sum_probs=17.8
Q ss_pred eecCCCccccccchhHhhhhcc
Q 040287 76 HECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
..|+.||+.| ..+.|.+|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4799999999 68899999764
No 47
>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=95.83 E-value=0.0027 Score=30.90 Aligned_cols=22 Identities=36% Similarity=0.694 Sum_probs=20.0
Q ss_pred eecCccCCccCChhHHHHHHHh
Q 040287 29 FECKTCNRQFPSFQALGGHRAS 50 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~ 50 (162)
|.|.+|++.|.....+..|+++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTS
T ss_pred CCcccCCCCcCCHHHHHHHHcc
Confidence 7899999999999999998764
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.12 E-value=0.02 Score=36.33 Aligned_cols=25 Identities=40% Similarity=0.692 Sum_probs=21.9
Q ss_pred eeecCccCCccCChhHHHHHHHhcC
Q 040287 28 VFECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
.+.|..|++.|.+...|..|++.+.
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCcc
Confidence 5999999999999999999999753
No 49
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=94.75 E-value=0.011 Score=46.90 Aligned_cols=61 Identities=25% Similarity=0.454 Sum_probs=50.5
Q ss_pred ceeecCccCCccCChhHHHHHHH--hcCCCCCCCCCCCCCcCccCCCCC--CceecC--CCccccccchhHhhhhccccc
Q 040287 27 RVFECKTCNRQFPSFQALGGHRA--SHKKPRLTDGTGGGADTQQSPAKP--RTHECS--VCGLEFAIGQALGGHMRRHRA 100 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~--~h~~~~~~~~~~~l~~h~~~h~~~--kp~~C~--~C~k~F~~~~~L~~H~~~H~~ 100 (162)
.++.|..|...|.....|..|.+ .|+ ++ +|+.|+ .|++.|.+...+.+|..+|++
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~-------------------~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 348 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHS-------------------GESLKPFSCPYSLCGKLFSRNDALKRHILLHTS 348 (467)
T ss_pred cCCCCccccCCccccccccccccccccc-------------------cccCCceeeeccCCCccccccccccCCcccccC
Confidence 46888888888888888777777 454 77 899999 799999999999999999988
Q ss_pred cccCCC
Q 040287 101 VALHGN 106 (162)
Q Consensus 101 ~~~~~~ 106 (162)
..+...
T Consensus 349 ~~~~~~ 354 (467)
T COG5048 349 ISPAKE 354 (467)
T ss_pred CCcccc
Confidence 876543
No 50
>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=94.31 E-value=0.04 Score=28.16 Aligned_cols=23 Identities=30% Similarity=0.521 Sum_probs=20.3
Q ss_pred eeecCccCCccCChhHHHHHHHh
Q 040287 28 VFECKTCNRQFPSFQALGGHRAS 50 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~ 50 (162)
+|.|++|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999989754
No 51
>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=94.26 E-value=0.028 Score=28.78 Aligned_cols=23 Identities=17% Similarity=0.541 Sum_probs=20.9
Q ss_pred ceecCCCccccccchhHhhhhcc
Q 040287 75 THECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68899999999999999999875
No 52
>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=93.23 E-value=0.077 Score=27.07 Aligned_cols=11 Identities=18% Similarity=0.809 Sum_probs=9.1
Q ss_pred eecCccCCccC
Q 040287 29 FECKTCNRQFP 39 (162)
Q Consensus 29 ~~C~~C~k~f~ 39 (162)
|+|.+||..+.
T Consensus 2 ~~C~~CGy~y~ 12 (33)
T cd00350 2 YVCPVCGYIYD 12 (33)
T ss_pred EECCCCCCEEC
Confidence 78999998764
No 53
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=93.23 E-value=0.085 Score=40.98 Aligned_cols=60 Identities=22% Similarity=0.398 Sum_probs=39.5
Q ss_pred CCCceecCC--CccccccchhHhhhhcc-ccccccCCCCcccccccCCCCchhhhcCCCcccccCCCCCCCCCchhhhhc
Q 040287 72 KPRTHECSV--CGLEFAIGQALGGHMRR-HRAVALHGNEKVSTLTLSDTAPLVKKANSRRVLCLDLNLTPYENDLECHRL 148 (162)
Q Consensus 72 ~~kp~~C~~--C~k~F~~~~~L~~H~~~-H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~nl~p~~~d~~~~~~ 148 (162)
++|||+|++ |.|++.....|+-|+.- |...+.+++.. ......+-..-.||.|+++-+++
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~-----------------p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPS-----------------PEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhccccCcccCCCCC-----------------ccccccccccCCceeccccchhh
Confidence 469999997 99999999999999874 54444432221 01111223444588888887766
No 54
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.61 E-value=0.13 Score=36.39 Aligned_cols=24 Identities=25% Similarity=0.801 Sum_probs=20.2
Q ss_pred ceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCc
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCG 82 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~ 82 (162)
+.|.|.+||..+. |+-|-.||+||
T Consensus 133 ~~~vC~vCGy~~~--------------------------------ge~P~~CPiCg 156 (166)
T COG1592 133 KVWVCPVCGYTHE--------------------------------GEAPEVCPICG 156 (166)
T ss_pred CEEEcCCCCCccc--------------------------------CCCCCcCCCCC
Confidence 3799999998743 77899999998
No 55
>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=91.42 E-value=0.18 Score=25.95 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=9.5
Q ss_pred eeecCccCCccC
Q 040287 28 VFECKTCNRQFP 39 (162)
Q Consensus 28 ~~~C~~C~k~f~ 39 (162)
.|+|.+||..+.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 589999998753
No 56
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=91.19 E-value=0.091 Score=39.22 Aligned_cols=49 Identities=29% Similarity=0.632 Sum_probs=38.6
Q ss_pred ceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccchhHhhh-hcccc
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGH-MRRHR 99 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H-~~~H~ 99 (162)
|++ |-.|++.|....-|-.|++. |-|+|.+|.|..-+...|..| |.+|.
T Consensus 10 kpw-cwycnrefddekiliqhqka-----------------------khfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 10 KPW-CWYCNREFDDEKILIQHQKA-----------------------KHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred Cce-eeecccccchhhhhhhhhhh-----------------------ccceeeeehhhhccCCCceeehhhhhh
Confidence 443 78899999888877777653 459999999988888889888 66664
No 57
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.61 E-value=0.091 Score=38.87 Aligned_cols=54 Identities=13% Similarity=0.282 Sum_probs=30.2
Q ss_pred CceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCc-----eecCCCccccccc
Q 040287 26 GRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRT-----HECSVCGLEFAIG 88 (162)
Q Consensus 26 ~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp-----~~C~~C~k~F~~~ 88 (162)
++...|++|++.|.++.-.....+.-... ..+.. ...+.-| ..|+.||.+|...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d------~D~~~---~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRD------SDFCP---RYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeec------CCCcc---ccCCCCCeeeeEEECCCCCCccccc
Confidence 46789999999998765433333221000 00000 0112333 5799999988755
No 58
>PRK04860 hypothetical protein; Provisional
Probab=90.35 E-value=0.15 Score=35.99 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=28.8
Q ss_pred CceecCCCccccccchhHhhhhccccccccCCCCcccc
Q 040287 74 RTHECSVCGLEFAIGQALGGHMRRHRAVALHGNEKVST 111 (162)
Q Consensus 74 kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~~~~~~~~ 111 (162)
-+|.|. |++ ....+.+|.++|+++++..|..+..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~ 151 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGE 151 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCc
Confidence 379998 997 7889999999999999987776544
No 59
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=89.79 E-value=0.23 Score=45.33 Aligned_cols=69 Identities=23% Similarity=0.393 Sum_probs=47.2
Q ss_pred CceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccchhHhhhhcc
Q 040287 26 GRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 26 ~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
..+|.|..|...|.....|..|.+.- .+..+......-+...+..-++| |..|...|+....|..||++
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~--~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKF--CFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHH--HhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHH
Confidence 34677777777777777777776221 11111222334455556667778 99999999999999999996
No 60
>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=88.05 E-value=0.3 Score=27.74 Aligned_cols=26 Identities=27% Similarity=0.497 Sum_probs=20.1
Q ss_pred ceecCCCccccccchhHhhhhcc-cccc
Q 040287 75 THECSVCGLEFAIGQALGGHMRR-HRAV 101 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~-H~~~ 101 (162)
.|.|++|++. -....|..|... |..+
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~ 28 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSE 28 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCC
Confidence 4899999995 456789999765 6554
No 61
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=87.78 E-value=0.21 Score=28.54 Aligned_cols=27 Identities=19% Similarity=0.409 Sum_probs=23.9
Q ss_pred CCCCceecCCCccccccchhHhhhhcc
Q 040287 71 AKPRTHECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 71 ~~~kp~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
-||.-+.|+.||..|.......+|...
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 478889999999999999999999753
No 62
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.51 E-value=0.48 Score=25.94 Aligned_cols=14 Identities=21% Similarity=0.726 Sum_probs=11.1
Q ss_pred ceeecCccCCccCC
Q 040287 27 RVFECKTCNRQFPS 40 (162)
Q Consensus 27 k~~~C~~C~k~f~~ 40 (162)
..|+|..||..|..
T Consensus 2 ~~y~C~~CG~~~~~ 15 (46)
T PRK00398 2 AEYKCARCGREVEL 15 (46)
T ss_pred CEEECCCCCCEEEE
Confidence 36899999988754
No 63
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=86.20 E-value=0.47 Score=26.47 Aligned_cols=25 Identities=28% Similarity=0.696 Sum_probs=19.8
Q ss_pred ceecCCCccccccc-----hhHhhhhc-ccc
Q 040287 75 THECSVCGLEFAIG-----QALGGHMR-RHR 99 (162)
Q Consensus 75 p~~C~~C~k~F~~~-----~~L~~H~~-~H~ 99 (162)
--.|..|++.++.. ++|.+|++ .|.
T Consensus 18 ~a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 18 RAKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 35699999998765 69999988 564
No 64
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=84.56 E-value=0.56 Score=26.85 Aligned_cols=31 Identities=13% Similarity=0.213 Sum_probs=26.2
Q ss_pred cccCCCceeecCccCCccCChhHHHHHHHhc
Q 040287 21 DMTAAGRVFECKTCNRQFPSFQALGGHRASH 51 (162)
Q Consensus 21 ~~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h 51 (162)
+..-||.-++|+-||..|....+..+|....
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKa 40 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNKA 40 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhHH
Confidence 4456788899999999999999999998643
No 65
>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=84.54 E-value=0.64 Score=30.58 Aligned_cols=16 Identities=31% Similarity=0.617 Sum_probs=13.4
Q ss_pred CCceecCCCccccccc
Q 040287 73 PRTHECSVCGLEFAIG 88 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~ 88 (162)
..|-.|++||..|.-.
T Consensus 24 k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 24 KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCccCCCCCCccCcc
Confidence 3588999999999766
No 66
>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=84.03 E-value=0.8 Score=24.70 Aligned_cols=25 Identities=20% Similarity=0.551 Sum_probs=16.6
Q ss_pred CCCceecCCCccccccc----hhHhhhhc
Q 040287 72 KPRTHECSVCGLEFAIG----QALGGHMR 96 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~----~~L~~H~~ 96 (162)
+..-..|..|++.+... ++|.+|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45667899999998774 78999984
No 67
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=80.95 E-value=1.1 Score=23.26 Aligned_cols=35 Identities=17% Similarity=0.443 Sum_probs=22.8
Q ss_pred eeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccc
Q 040287 28 VFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFA 86 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~ 86 (162)
.+.|+.|+..|.-..... .. ......|+.|+..|.
T Consensus 2 ~~~CP~C~~~~~v~~~~~-----~~-------------------~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQL-----GA-------------------NGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHc-----CC-------------------CCCEEECCCCCCEEE
Confidence 368999999887554311 00 122578999998874
No 68
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=80.02 E-value=0.95 Score=28.42 Aligned_cols=19 Identities=32% Similarity=0.620 Sum_probs=14.6
Q ss_pred CCCceecCCCccccccchh
Q 040287 72 KPRTHECSVCGLEFAIGQA 90 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~~~ 90 (162)
+...+.|..||..|+-...
T Consensus 50 a~GIW~C~kCg~~fAGgay 68 (89)
T COG1997 50 ATGIWKCRKCGAKFAGGAY 68 (89)
T ss_pred ccCeEEcCCCCCeeccccc
Confidence 3457999999999985543
No 69
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=80.00 E-value=2 Score=29.71 Aligned_cols=40 Identities=20% Similarity=0.491 Sum_probs=26.2
Q ss_pred CCCceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccc
Q 040287 24 AAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFA 86 (162)
Q Consensus 24 ~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~ 86 (162)
.+..-|.|+.|+..|.....+..- + .+..|.|+.||....
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ea~~~~---d--------------------~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFLEANQLL---D--------------------MDGTFTCPRCGEELE 134 (147)
T ss_pred cCCcEEECcCCCCEeeHHHHHHhc---C--------------------CCCcEECCCCCCEEE
Confidence 345679999999999854432210 1 122399999997654
No 70
>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=79.41 E-value=0.6 Score=25.11 Aligned_cols=13 Identities=23% Similarity=0.920 Sum_probs=10.9
Q ss_pred eeecCccCCccCC
Q 040287 28 VFECKTCNRQFPS 40 (162)
Q Consensus 28 ~~~C~~C~k~f~~ 40 (162)
.|+|..||..|..
T Consensus 5 ey~C~~Cg~~fe~ 17 (42)
T PF09723_consen 5 EYRCEECGHEFEV 17 (42)
T ss_pred EEEeCCCCCEEEE
Confidence 4899999998864
No 71
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=78.55 E-value=1.9 Score=24.14 Aligned_cols=13 Identities=23% Similarity=0.731 Sum_probs=11.2
Q ss_pred CceeecCccCCcc
Q 040287 26 GRVFECKTCNRQF 38 (162)
Q Consensus 26 ~k~~~C~~C~k~f 38 (162)
...|+|..||+.|
T Consensus 4 ~~~Y~C~~Cg~~~ 16 (49)
T COG1996 4 MMEYKCARCGREV 16 (49)
T ss_pred eEEEEhhhcCCee
Confidence 4579999999998
No 72
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=78.14 E-value=1.6 Score=32.94 Aligned_cols=49 Identities=18% Similarity=0.426 Sum_probs=36.4
Q ss_pred eeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccchhHhhhhccc
Q 040287 28 VFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGHMRRH 98 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H~~~H 98 (162)
-|.|..||..-. +..+.+|+-.-+ + .-|.|--||+.|-+ .....|..--
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCr-------------------n-~~fSCIDC~k~F~~-~sYknH~kCI 51 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCR-------------------N-AYFSCIDCGKTFER-VSYKNHTKCI 51 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhcc-------------------C-CeeEEeeccccccc-chhhhhhhhc
Confidence 388999998866 445677775543 3 46999999999987 6677786643
No 73
>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=76.82 E-value=0.93 Score=25.34 Aligned_cols=13 Identities=23% Similarity=0.904 Sum_probs=11.0
Q ss_pred eeecCccCCccCC
Q 040287 28 VFECKTCNRQFPS 40 (162)
Q Consensus 28 ~~~C~~C~k~f~~ 40 (162)
.|+|..||..|..
T Consensus 5 ey~C~~Cg~~fe~ 17 (52)
T TIGR02605 5 EYRCTACGHRFEV 17 (52)
T ss_pred EEEeCCCCCEeEE
Confidence 5899999998864
No 74
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=76.41 E-value=0.94 Score=35.81 Aligned_cols=69 Identities=17% Similarity=0.338 Sum_probs=41.9
Q ss_pred CceeecCc--cCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccccchhHhhh
Q 040287 26 GRVFECKT--CNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFAIGQALGGH 94 (162)
Q Consensus 26 ~k~~~C~~--C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~L~~H 94 (162)
.++|+|.+ |.+.++....|..|...-+...---..-.-.-|.-.-...|||.|++|.+++.....|+-|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 46899965 8999888877777754322110000000112233333457999999999998877776655
No 75
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=75.56 E-value=1.9 Score=30.95 Aligned_cols=34 Identities=24% Similarity=0.528 Sum_probs=25.9
Q ss_pred CCceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccc
Q 040287 25 AGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFA 86 (162)
Q Consensus 25 ~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~ 86 (162)
+..-|.|+.|+..|..-.++. --|.|+.||-...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~----------------------------~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME----------------------------YGFRCPQCGEMLE 147 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh----------------------------cCCcCCCCCCCCe
Confidence 446799999999998776542 1599999997654
No 76
>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=74.89 E-value=2 Score=30.25 Aligned_cols=35 Identities=20% Similarity=0.415 Sum_probs=27.0
Q ss_pred CCCceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccc
Q 040287 24 AAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFA 86 (162)
Q Consensus 24 ~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~ 86 (162)
++..-|.|+.|+..|+.-.++. --|.|+.||....
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~----------------------------~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAME----------------------------LNFTCPRCGAMLD 139 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHH----------------------------cCCcCCCCCCEee
Confidence 4456799999999998877754 1499999997653
No 77
>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=73.99 E-value=2.4 Score=28.66 Aligned_cols=20 Identities=25% Similarity=0.277 Sum_probs=14.9
Q ss_pred CCceecCCCccccccchhHh
Q 040287 73 PRTHECSVCGLEFAIGQALG 92 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~ 92 (162)
..|-.|++||..|.-...++
T Consensus 24 k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 24 RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred CCCccCCCcCCccCcchhhc
Confidence 45889999999987654433
No 78
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=73.97 E-value=0.69 Score=32.43 Aligned_cols=21 Identities=29% Similarity=0.510 Sum_probs=15.6
Q ss_pred CceecCCCccccccchhHhhh
Q 040287 74 RTHECSVCGLEFAIGQALGGH 94 (162)
Q Consensus 74 kp~~C~~C~k~F~~~~~L~~H 94 (162)
+.+.|+.||++|.+-..+..-
T Consensus 27 ~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 27 RRRECLACGKRFTTFERVELV 47 (154)
T ss_pred eeeeccccCCcceEeEeccCc
Confidence 348999999999876554433
No 79
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=73.92 E-value=2.5 Score=28.89 Aligned_cols=27 Identities=22% Similarity=0.482 Sum_probs=17.3
Q ss_pred CCceeecCccCCccCChhHHHHHHHhcCCC
Q 040287 25 AGRVFECKTCNRQFPSFQALGGHRASHKKP 54 (162)
Q Consensus 25 ~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~ 54 (162)
.+.--.|-+||+.|+. |++|.+.|.|-
T Consensus 69 ~~d~i~clecGk~~k~---LkrHL~~~~gl 95 (132)
T PF05443_consen 69 TPDYIICLECGKKFKT---LKRHLRTHHGL 95 (132)
T ss_dssp -SS-EE-TBT--EESB---HHHHHHHTT-S
T ss_pred ccCeeEEccCCcccch---HHHHHHHccCC
Confidence 4456899999999975 69999999754
No 80
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=73.91 E-value=2.6 Score=21.92 Aligned_cols=34 Identities=26% Similarity=0.552 Sum_probs=23.1
Q ss_pred eecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccc
Q 040287 29 FECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFA 86 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~ 86 (162)
..|+.|+..|.-...- .- .+.+..+|+.|+..|.
T Consensus 3 i~CP~C~~~f~v~~~~-----l~-------------------~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDK-----LP-------------------AGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHH-----cc-------------------cCCcEEECCCCCcEee
Confidence 4789999988755431 11 1345789999998874
No 81
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=72.88 E-value=3.5 Score=22.45 Aligned_cols=13 Identities=23% Similarity=0.736 Sum_probs=10.6
Q ss_pred eeecCccCCccCC
Q 040287 28 VFECKTCNRQFPS 40 (162)
Q Consensus 28 ~~~C~~C~k~f~~ 40 (162)
.|.|..||..|..
T Consensus 2 ~Y~C~~Cg~~~~~ 14 (44)
T smart00659 2 IYICGECGRENEI 14 (44)
T ss_pred EEECCCCCCEeec
Confidence 4899999988763
No 82
>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=71.21 E-value=2.6 Score=20.15 Aligned_cols=20 Identities=25% Similarity=0.517 Sum_probs=15.4
Q ss_pred eecCCCccccccchhHhhhhc
Q 040287 76 HECSVCGLEFAIGQALGGHMR 96 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~ 96 (162)
..|++|++.+ ....+.+|..
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 5577777765
No 83
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=70.71 E-value=3.2 Score=21.49 Aligned_cols=34 Identities=26% Similarity=0.520 Sum_probs=22.7
Q ss_pred eecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccccc
Q 040287 29 FECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLEFA 86 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~F~ 86 (162)
..|+.|+..|.-....- - ...+..+|+.|+..|.
T Consensus 3 i~Cp~C~~~y~i~d~~i-----p-------------------~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKI-----P-------------------PKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEEeCCHHHC-----C-------------------CCCcEEECCCCCCEeC
Confidence 57899998887654311 1 1334678999998873
No 84
>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=70.35 E-value=2.5 Score=27.54 Aligned_cols=72 Identities=15% Similarity=0.251 Sum_probs=45.6
Q ss_pred CCceeecCccCCccCChhHHHHHHHh-cCCCCCCC--------CCC--------CC---------CcCccCCCCCCceec
Q 040287 25 AGRVFECKTCNRQFPSFQALGGHRAS-HKKPRLTD--------GTG--------GG---------ADTQQSPAKPRTHEC 78 (162)
Q Consensus 25 ~~k~~~C~~C~k~f~~~~~L~~H~~~-h~~~~~~~--------~~~--------~l---------~~h~~~h~~~kp~~C 78 (162)
.-+...|..|+..... +.+..|.+. |....... ... .+ .....++ .-|.|
T Consensus 8 ~~~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~---~G~~C 83 (109)
T PF12013_consen 8 EYRVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVY---DGYRC 83 (109)
T ss_pred cCCEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCC---CCeee
Confidence 3467899999987765 778889874 32211110 000 00 0111122 34899
Q ss_pred ----CCCccccccchhHhhhhccccc
Q 040287 79 ----SVCGLEFAIGQALGGHMRRHRA 100 (162)
Q Consensus 79 ----~~C~k~F~~~~~L~~H~~~H~~ 100 (162)
..|+..+.+...+.+|.+.++|
T Consensus 84 ~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 84 QCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred ecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 9999999999999999987654
No 85
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=69.93 E-value=1.9 Score=29.46 Aligned_cols=28 Identities=32% Similarity=0.638 Sum_probs=17.4
Q ss_pred CCceecCCCccccccchhHhhhhcccccccc
Q 040287 73 PRTHECSVCGLEFAIGQALGGHMRRHRAVAL 103 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~ 103 (162)
+.--.|-+||+.|.. |++|.+.|+|..|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 445679999999974 5999999977655
No 86
>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=68.22 E-value=4.9 Score=26.15 Aligned_cols=26 Identities=15% Similarity=0.302 Sum_probs=23.0
Q ss_pred eeec----CccCCccCChhHHHHHHHhcCC
Q 040287 28 VFEC----KTCNRQFPSFQALGGHRASHKK 53 (162)
Q Consensus 28 ~~~C----~~C~k~f~~~~~L~~H~~~h~~ 53 (162)
-|.| ..|++...+...+..|.+.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999987653
No 87
>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=67.17 E-value=4.9 Score=26.63 Aligned_cols=35 Identities=11% Similarity=0.336 Sum_probs=21.9
Q ss_pred hhhhcCCCCCCccccccccCCCceeecCccCCccCC
Q 040287 5 LMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 5 ~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~ 40 (162)
-..++.+..+. .....+..-.-...|..|+..|..
T Consensus 48 f~~~~~~t~~e-ga~L~I~~~p~~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 48 FEVVREGTVAE-GAKLNIEDEPVECECEDCSEEVSP 82 (115)
T ss_pred HHHHhCCCccC-CCEEEEEeeCcEEEcccCCCEEec
Confidence 33444444443 344556666667999999988764
No 88
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=67.17 E-value=5.1 Score=26.65 Aligned_cols=34 Identities=18% Similarity=0.319 Sum_probs=20.6
Q ss_pred hhcCCCCCCccccccccCCCceeecCccCCccCC
Q 040287 7 FMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 7 ~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~ 40 (162)
.++.+..+-...-..+..-.-.+.|..||..|..
T Consensus 50 ~~~~~T~~~ega~L~Ie~vp~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 50 TFREESLVCKDAILDIVDEKVELECKDCSHVFKP 83 (117)
T ss_pred HHhcCCcccCCCEEEEEecCCEEEhhhCCCcccc
Confidence 3444442222344455666667999999988753
No 89
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=66.72 E-value=6 Score=29.31 Aligned_cols=29 Identities=14% Similarity=0.335 Sum_probs=22.0
Q ss_pred CCCceeecCccCCccCChhHHHHHHHhcC
Q 040287 24 AAGRVFECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 24 ~~~k~~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
.++..|.|.+|+|.|+-...+..|+..-+
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~nKH 101 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIFNKH 101 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHHHH-
T ss_pred HcCCEECCCCCCcccCChHHHHHHHhhcC
Confidence 34567999999999999999999986543
No 90
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=66.49 E-value=2.7 Score=26.65 Aligned_cols=19 Identities=21% Similarity=0.232 Sum_probs=14.4
Q ss_pred CCCceecCCCccccccchh
Q 040287 72 KPRTHECSVCGLEFAIGQA 90 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~~~ 90 (162)
+...+.|..|++.|+-...
T Consensus 51 a~GIW~C~~C~~~~AGGAy 69 (90)
T PTZ00255 51 AVGIWRCKGCKKTVAGGAW 69 (90)
T ss_pred eeEEEEcCCCCCEEeCCcc
Confidence 4457999999999975543
No 91
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=66.26 E-value=3.3 Score=20.27 Aligned_cols=20 Identities=25% Similarity=0.596 Sum_probs=13.3
Q ss_pred eecCCCccccccchhHhhhhc
Q 040287 76 HECSVCGLEFAIGQALGGHMR 96 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~ 96 (162)
|.|-.|++.| .....+.|..
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht~ 20 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHTS 20 (28)
T ss_dssp EEETTTTEEE-EGGGTTT---
T ss_pred CeeecCCCCc-CcCCcCCCCc
Confidence 5799999999 5566666643
No 92
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=65.89 E-value=5.4 Score=26.38 Aligned_cols=33 Identities=9% Similarity=0.117 Sum_probs=19.5
Q ss_pred hhcCCCCCCccccccccCCCceeecCccCCccCC
Q 040287 7 FMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 7 ~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~ 40 (162)
.++.+..+. .+-..+..-.-.+.|..||..|..
T Consensus 50 ~~~~~T~~e-gA~L~I~~vp~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 50 IVCHGTVAQ-GCDLHIVYKPAQAWCWDCSQVVEI 82 (113)
T ss_pred HHhCCCccC-CCEEEEEeeCcEEEcccCCCEEec
Confidence 344444332 333345555567999999988753
No 93
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=65.59 E-value=2.3 Score=26.94 Aligned_cols=16 Identities=38% Similarity=0.781 Sum_probs=12.2
Q ss_pred CCceecCCCccccccc
Q 040287 73 PRTHECSVCGLEFAIG 88 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~ 88 (162)
.-.+.|..|++.|+..
T Consensus 51 ~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 51 TGIWKCKKCGKKFAGG 66 (90)
T ss_dssp TTEEEETTTTEEEE-B
T ss_pred eEEeecCCCCCEEeCC
Confidence 3469999999999754
No 94
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=65.27 E-value=8.8 Score=22.33 Aligned_cols=10 Identities=30% Similarity=0.962 Sum_probs=8.5
Q ss_pred CceecCCCcc
Q 040287 74 RTHECSVCGL 83 (162)
Q Consensus 74 kp~~C~~C~k 83 (162)
.+|.|+.||.
T Consensus 49 ~~Y~Cp~CGF 58 (61)
T COG2888 49 NPYRCPKCGF 58 (61)
T ss_pred CceECCCcCc
Confidence 4899999985
No 95
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=64.99 E-value=3.2 Score=28.34 Aligned_cols=25 Identities=24% Similarity=0.373 Sum_probs=21.4
Q ss_pred eecCCCccccccchhHhhhhcccccccc
Q 040287 76 HECSVCGLEFAIGQALGGHMRRHRAVAL 103 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~H~~~~~ 103 (162)
..|-++|+.|. .|++|+.+|.+..|
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 46999999996 79999999988766
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=64.42 E-value=4.9 Score=23.33 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=8.5
Q ss_pred CceecCCCcc
Q 040287 74 RTHECSVCGL 83 (162)
Q Consensus 74 kp~~C~~C~k 83 (162)
.+|.|+.||.
T Consensus 47 ~~Y~CP~CGF 56 (59)
T PRK14890 47 NPYTCPKCGF 56 (59)
T ss_pred CceECCCCCC
Confidence 4899999985
No 97
>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=62.68 E-value=3.8 Score=19.61 Aligned_cols=11 Identities=36% Similarity=1.041 Sum_probs=8.9
Q ss_pred eecCCCccccc
Q 040287 76 HECSVCGLEFA 86 (162)
Q Consensus 76 ~~C~~C~k~F~ 86 (162)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 46899999885
No 98
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.31 E-value=7.3 Score=33.72 Aligned_cols=21 Identities=29% Similarity=0.460 Sum_probs=13.4
Q ss_pred ecCCCccccccchhHhhhhcc
Q 040287 77 ECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 77 ~C~~C~k~F~~~~~L~~H~~~ 97 (162)
.|..|...|-....|.+|++.
T Consensus 184 ~C~~C~~~fld~~el~rH~~~ 204 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRF 204 (669)
T ss_pred cchhhhhhhccHHHHHHhhcc
Confidence 466666666666666666664
No 99
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=62.23 E-value=1.6 Score=37.74 Aligned_cols=26 Identities=23% Similarity=0.712 Sum_probs=23.7
Q ss_pred ceeecCccCCccCChhHHHHHHHhcC
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
..|.|.+|+|.|....++..||++|.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr 816 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHR 816 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHH
Confidence 35999999999999999999999995
No 100
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.33 E-value=6.9 Score=26.74 Aligned_cols=22 Identities=14% Similarity=0.504 Sum_probs=16.1
Q ss_pred ccccCCCceeecCccCCccCCh
Q 040287 20 VDMTAAGRVFECKTCNRQFPSF 41 (162)
Q Consensus 20 ~~~h~~~k~~~C~~C~k~f~~~ 41 (162)
..+......+.|..||..|...
T Consensus 62 L~i~~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 62 IIFEEEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred EEEEecceEEECCCCCCEEecc
Confidence 3444555779999999988653
No 101
>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=61.28 E-value=3.4 Score=26.26 Aligned_cols=19 Identities=32% Similarity=0.606 Sum_probs=14.3
Q ss_pred CCCceecCCCccccccchh
Q 040287 72 KPRTHECSVCGLEFAIGQA 90 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~~~ 90 (162)
+...+.|..|++.|+-...
T Consensus 50 a~GIW~C~~C~~~~AGGAy 68 (91)
T TIGR00280 50 STGIWTCRKCGAKFAGGAY 68 (91)
T ss_pred eeEEEEcCCCCCEEeCCcc
Confidence 3457999999999975543
No 102
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=60.97 E-value=4.7 Score=25.54 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=11.2
Q ss_pred ceeecCccCCccCC
Q 040287 27 RVFECKTCNRQFPS 40 (162)
Q Consensus 27 k~~~C~~C~k~f~~ 40 (162)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 47789999998864
No 103
>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=60.41 E-value=4.6 Score=19.00 Aligned_cols=10 Identities=30% Similarity=0.909 Sum_probs=8.3
Q ss_pred CceecCCCcc
Q 040287 74 RTHECSVCGL 83 (162)
Q Consensus 74 kp~~C~~C~k 83 (162)
.+|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4799999984
No 104
>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=60.26 E-value=7.4 Score=19.61 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=7.7
Q ss_pred ceecCCCcccc
Q 040287 75 THECSVCGLEF 85 (162)
Q Consensus 75 p~~C~~C~k~F 85 (162)
+-.|+.||...
T Consensus 17 ~irC~~CG~RI 27 (32)
T PF03604_consen 17 PIRCPECGHRI 27 (32)
T ss_dssp TSSBSSSS-SE
T ss_pred cEECCcCCCeE
Confidence 56899998654
No 105
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=59.15 E-value=8.6 Score=25.45 Aligned_cols=35 Identities=14% Similarity=0.366 Sum_probs=20.5
Q ss_pred hhhhhcCCCCCCccccccccCCCceeecCccCCccC
Q 040287 4 CLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFP 39 (162)
Q Consensus 4 C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~ 39 (162)
|-..+..+.-+. ..-..+..-.-.+.|..|+..|.
T Consensus 47 ~f~~~~~~t~~e-gA~L~i~~~p~~~~C~~Cg~~~~ 81 (114)
T PRK03681 47 CFDLVCRGTVAE-GCKLHLEEQEAECWCETCQQYVT 81 (114)
T ss_pred HHHHHhCCCccC-CCEEEEEeeCcEEEcccCCCeee
Confidence 333444444332 34444555566799999998764
No 106
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=58.64 E-value=8.3 Score=30.69 Aligned_cols=70 Identities=21% Similarity=0.315 Sum_probs=45.3
Q ss_pred eeecCc--cCCccCChhHHHHHHHhcCCC----------CCCCCC------CCCCcCccCCC---CCCce-ecCCCcccc
Q 040287 28 VFECKT--CNRQFPSFQALGGHRASHKKP----------RLTDGT------GGGADTQQSPA---KPRTH-ECSVCGLEF 85 (162)
Q Consensus 28 ~~~C~~--C~k~f~~~~~L~~H~~~h~~~----------~~~~~~------~~l~~h~~~h~---~~kp~-~C~~C~k~F 85 (162)
.|.|+. |..+......|..|.++.++. +.|.++ ..|..|..... |-|-+ .|..|...|
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~F 230 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYF 230 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhcccee
Confidence 377754 666666677888887764432 222222 24566665433 33433 499999999
Q ss_pred ccchhHhhhhcc
Q 040287 86 AIGQALGGHMRR 97 (162)
Q Consensus 86 ~~~~~L~~H~~~ 97 (162)
-..+.|.+|+|.
T Consensus 231 YdDDEL~~HcR~ 242 (493)
T COG5236 231 YDDDELRRHCRL 242 (493)
T ss_pred cChHHHHHHHHh
Confidence 999999999985
No 107
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=58.35 E-value=3.7 Score=30.32 Aligned_cols=25 Identities=32% Similarity=0.691 Sum_probs=19.7
Q ss_pred CCceecCCCccccccchhHhhhhcc
Q 040287 73 PRTHECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
+|...|++|++.|.++.-+.+..+.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 4678999999999988766666553
No 108
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=57.97 E-value=3.9 Score=30.28 Aligned_cols=30 Identities=17% Similarity=0.347 Sum_probs=22.5
Q ss_pred CCCceecCCCccccccchhHhhhhcccccc
Q 040287 72 KPRTHECSVCGLEFAIGQALGGHMRRHRAV 101 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~~~L~~H~~~H~~~ 101 (162)
++..|.|+.|+|.|.-..-..+|+...+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 455699999999999999999998864443
No 109
>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=57.21 E-value=5.6 Score=20.68 Aligned_cols=15 Identities=33% Similarity=0.698 Sum_probs=11.6
Q ss_pred ceecCCCccccccch
Q 040287 75 THECSVCGLEFAIGQ 89 (162)
Q Consensus 75 p~~C~~C~k~F~~~~ 89 (162)
-|.|..||..|....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 488999999886443
No 110
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.95 E-value=2.7 Score=30.84 Aligned_cols=60 Identities=23% Similarity=0.357 Sum_probs=41.1
Q ss_pred eecCccCCccCChhHHHHHHHh-cCCCCCCCCCCCCCcCccCCCCCCceecC--CCccccccchhHhhhhc-cc
Q 040287 29 FECKTCNRQFPSFQALGGHRAS-HKKPRLTDGTGGGADTQQSPAKPRTHECS--VCGLEFAIGQALGGHMR-RH 98 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~-h~~~~~~~~~~~l~~h~~~h~~~kp~~C~--~C~k~F~~~~~L~~H~~-~H 98 (162)
..|.+|.+.|.+..-|..|+.. |.. + -...+-.|.--|+|- .|+..|.+....+.|+- .|
T Consensus 107 ~sCs~C~r~~Pt~hLLd~HI~E~HDs---------~-Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 107 NSCSFCKRAFPTGHLLDAHILEWHDS---------L-FQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred chhHHHHHhCCchhhhhHHHHHHHHH---------H-HHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 3799999999999988888742 210 0 000111255578995 49999999999999964 45
No 111
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.81 E-value=5.7 Score=26.12 Aligned_cols=16 Identities=6% Similarity=0.048 Sum_probs=12.9
Q ss_pred CCCceecCCCcccccc
Q 040287 72 KPRTHECSVCGLEFAI 87 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~ 87 (162)
...|..|++||++|..
T Consensus 23 NrdPiVsPytG~s~P~ 38 (129)
T COG4530 23 NRDPIVSPYTGKSYPR 38 (129)
T ss_pred CCCccccCcccccchH
Confidence 3468899999999953
No 112
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=56.04 E-value=5.5 Score=25.66 Aligned_cols=22 Identities=14% Similarity=0.262 Sum_probs=17.5
Q ss_pred ccccccCCCceeecCccCCccCC
Q 040287 18 NSVDMTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 18 ~h~~~h~~~k~~~C~~C~k~f~~ 40 (162)
..+..+.+ ++++|..||..|.-
T Consensus 70 ~W~~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 70 IWMWLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEEEEeCC-CceeCCCCCcEEEE
Confidence 45567777 79999999998863
No 113
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=55.64 E-value=4.5 Score=25.68 Aligned_cols=18 Identities=39% Similarity=0.726 Sum_probs=13.7
Q ss_pred CCCceecCCCccccccch
Q 040287 72 KPRTHECSVCGLEFAIGQ 89 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~~ 89 (162)
+.-.+.|..|++.|+-..
T Consensus 51 a~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 51 GTGIWECRKCGAKFAGGA 68 (90)
T ss_pred EEEEEEcCCCCCEEeCCc
Confidence 345799999999997544
No 114
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=55.27 E-value=3.9 Score=27.00 Aligned_cols=35 Identities=11% Similarity=0.382 Sum_probs=18.6
Q ss_pred hhhcCCCCCCccccccccCCCceeecCccCCccCCh
Q 040287 6 MFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQFPSF 41 (162)
Q Consensus 6 k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f~~~ 41 (162)
..++.+..+. ..-..+..-.-.+.|..||+.|...
T Consensus 49 ~~~~~~T~~e-~a~L~Ie~~p~~~~C~~Cg~~~~~~ 83 (113)
T PF01155_consen 49 EVLAEGTILE-GAELEIEEVPARARCRDCGHEFEPD 83 (113)
T ss_dssp HHHHCCSTTT-T-EEEEEEE--EEEETTTS-EEECH
T ss_pred HHHhCCCCcc-CCEEEEEecCCcEECCCCCCEEecC
Confidence 3444444332 3334445555569999999998754
No 115
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=54.60 E-value=12 Score=25.52 Aligned_cols=56 Identities=16% Similarity=0.246 Sum_probs=32.1
Q ss_pred ccCCCceeecCccCCccCChhHHHHHHHhcCCCCCCC-------CCCCCCcCccCCCCCCceecCCCccccccchh
Q 040287 22 MTAAGRVFECKTCNRQFPSFQALGGHRASHKKPRLTD-------GTGGGADTQQSPAKPRTHECSVCGLEFAIGQA 90 (162)
Q Consensus 22 ~h~~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~-------~~~~l~~h~~~h~~~kp~~C~~C~k~F~~~~~ 90 (162)
.-.+.+.|.|.+|..++.....|+ +.... |-..|.+|-..|. .|+.|..+|.+++.
T Consensus 74 vF~d~~lYeCnIC~etS~ee~FLK--------PneCCgY~iCn~Cya~LWK~~~~yp-----vCPvCkTSFKss~~ 136 (140)
T PF05290_consen 74 VFLDPKLYECNICKETSAEERFLK--------PNECCGYSICNACYANLWKFCNLYP-----VCPVCKTSFKSSSS 136 (140)
T ss_pred eecCCCceeccCcccccchhhcCC--------cccccchHHHHHHHHHHHHHcccCC-----CCCccccccccccc
Confidence 345668899999998865433221 11111 1113344433222 69999999987653
No 116
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=54.06 E-value=4.2 Score=24.69 Aligned_cols=20 Identities=30% Similarity=0.659 Sum_probs=15.6
Q ss_pred CCCceecC--CCccccccchhH
Q 040287 72 KPRTHECS--VCGLEFAIGQAL 91 (162)
Q Consensus 72 ~~kp~~C~--~C~k~F~~~~~L 91 (162)
.++-+.|. .||.+|.....+
T Consensus 24 ~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 24 KERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred heeeeecCCCCCCCEEEEEEEE
Confidence 46678998 899999876554
No 117
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=53.93 E-value=3.8 Score=32.82 Aligned_cols=70 Identities=21% Similarity=0.365 Sum_probs=44.6
Q ss_pred eeecCccCCccCChhHHHHHHHh--cCC---CC----CCCC------CC-CC--CcCccCCCCCCceecCCCccccccch
Q 040287 28 VFECKTCNRQFPSFQALGGHRAS--HKK---PR----LTDG------TG-GG--ADTQQSPAKPRTHECSVCGLEFAIGQ 89 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~--h~~---~~----~~~~------~~-~l--~~h~~~h~~~kp~~C~~C~k~F~~~~ 89 (162)
.|.|..|...|.....-+.|.++ |.- .+ |-.. +. .. ..-...-.++-++.|..|.++|+...
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lPPItaE~F~~k~~s~~~~~~~~~e~~~~~~~c~~c~k~~~s~~ 82 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLPPITAEEFNEKVLSDDSEKEENLEEAESVVYCEACNKSFASPK 82 (390)
T ss_pred cceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCCCcCHHHHhHHHhhhhhhhhhhhhhcccceehHHhhccccChh
Confidence 48999999999998877778764 321 11 1000 00 00 00000123456799999999999999
Q ss_pred hHhhhhcc
Q 040287 90 ALGGHMRR 97 (162)
Q Consensus 90 ~L~~H~~~ 97 (162)
....|+..
T Consensus 83 a~~~hl~S 90 (390)
T KOG2785|consen 83 AHENHLKS 90 (390)
T ss_pred hHHHHHHH
Confidence 99999875
No 118
>PHA00626 hypothetical protein
Probab=52.99 E-value=7.7 Score=22.28 Aligned_cols=15 Identities=20% Similarity=0.399 Sum_probs=12.4
Q ss_pred CceecCCCccccccc
Q 040287 74 RTHECSVCGLEFAIG 88 (162)
Q Consensus 74 kp~~C~~C~k~F~~~ 88 (162)
..|+|+.||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 479999999999743
No 119
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=51.86 E-value=8.2 Score=20.32 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=12.0
Q ss_pred ceecCCCccccccc
Q 040287 75 THECSVCGLEFAIG 88 (162)
Q Consensus 75 p~~C~~C~k~F~~~ 88 (162)
||.|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999999643
No 120
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.85 E-value=8.9 Score=31.34 Aligned_cols=19 Identities=16% Similarity=0.274 Sum_probs=14.6
Q ss_pred CCCceecCCCccccccchh
Q 040287 72 KPRTHECSVCGLEFAIGQA 90 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~~~ 90 (162)
|..-|+|+.||+.++...-
T Consensus 364 G~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 364 GRNGFRCKKCGTRARETLI 382 (421)
T ss_pred CCCCcccccccccCCcccc
Confidence 4448999999999876543
No 121
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=51.72 E-value=7.4 Score=26.48 Aligned_cols=15 Identities=40% Similarity=0.957 Sum_probs=12.7
Q ss_pred ceecCCCccccccch
Q 040287 75 THECSVCGLEFAIGQ 89 (162)
Q Consensus 75 p~~C~~C~k~F~~~~ 89 (162)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 688999999998765
No 122
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=51.13 E-value=11 Score=30.88 Aligned_cols=24 Identities=21% Similarity=0.523 Sum_probs=17.6
Q ss_pred ccCCCceeecCccCCccCChhHHH
Q 040287 22 MTAAGRVFECKTCNRQFPSFQALG 45 (162)
Q Consensus 22 ~h~~~k~~~C~~C~k~f~~~~~L~ 45 (162)
.-+...-|.|+.|.+.|..-..++
T Consensus 122 d~t~~~~Y~Cp~C~kkyt~Lea~~ 145 (436)
T KOG2593|consen 122 DDTNVAGYVCPNCQKKYTSLEALQ 145 (436)
T ss_pred hccccccccCCccccchhhhHHHH
Confidence 344566799999999997655543
No 123
>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=50.69 E-value=9.5 Score=20.31 Aligned_cols=13 Identities=23% Similarity=0.728 Sum_probs=10.8
Q ss_pred CceecCCCccccc
Q 040287 74 RTHECSVCGLEFA 86 (162)
Q Consensus 74 kp~~C~~C~k~F~ 86 (162)
++-.|++||..|.
T Consensus 28 ~~~~CpYCg~~yv 40 (40)
T PF10276_consen 28 GPVVCPYCGTRYV 40 (40)
T ss_dssp CEEEETTTTEEEE
T ss_pred CeEECCCCCCEEC
Confidence 5789999999873
No 124
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=50.62 E-value=10 Score=22.22 Aligned_cols=15 Identities=33% Similarity=0.709 Sum_probs=7.7
Q ss_pred CCceecCCCcccccc
Q 040287 73 PRTHECSVCGLEFAI 87 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~ 87 (162)
.+.+-|..||..|-.
T Consensus 23 ~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 23 RRRHHCRNCGRVVCS 37 (69)
T ss_dssp S-EEE-TTT--EEEC
T ss_pred eeeEccCCCCCEECC
Confidence 346778888887753
No 125
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=50.41 E-value=3.6 Score=30.95 Aligned_cols=30 Identities=23% Similarity=0.444 Sum_probs=22.3
Q ss_pred ccCCCceeecCccCCccCChhHHHHHH-Hhc
Q 040287 22 MTAAGRVFECKTCNRQFPSFQALGGHR-ASH 51 (162)
Q Consensus 22 ~h~~~k~~~C~~C~k~f~~~~~L~~H~-~~h 51 (162)
.|...|.|+|.+|.|..-+--.|..|- .+|
T Consensus 28 qhqkakhfkchichkkl~sgpglsihcmqvh 58 (341)
T KOG2893|consen 28 QHQKAKHFKCHICHKKLFSGPGLSIHCMQVH 58 (341)
T ss_pred hhhhhccceeeeehhhhccCCCceeehhhhh
Confidence 355678899999998877777777773 444
No 126
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=49.59 E-value=9.7 Score=26.61 Aligned_cols=36 Identities=17% Similarity=0.552 Sum_probs=22.8
Q ss_pred CCceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccc
Q 040287 25 AGRVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLE 84 (162)
Q Consensus 25 ~~k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~ 84 (162)
...+|.|. |+..|.+.. +|-.+ -.|+ -|.|..|+-.
T Consensus 114 ~~~~Y~C~-C~q~~l~~R---Rhn~~-------------------~~g~-~YrC~~C~gk 149 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRIR---RHNTV-------------------RRGE-VYRCGKCGGK 149 (156)
T ss_pred cceeEEee-cCCccchhh---hcccc-------------------cccc-eEEeccCCce
Confidence 34579999 998875432 22111 1266 8999999754
No 127
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=48.88 E-value=18 Score=19.22 Aligned_cols=24 Identities=25% Similarity=0.412 Sum_probs=17.6
Q ss_pred eecCccCCccC--ChhHHHHHHHhcC
Q 040287 29 FECKTCNRQFP--SFQALGGHRASHK 52 (162)
Q Consensus 29 ~~C~~C~k~f~--~~~~L~~H~~~h~ 52 (162)
-.|..||-.|. ....-..|.+.|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 58999998886 4455666777664
No 128
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=48.19 E-value=9.6 Score=32.36 Aligned_cols=29 Identities=28% Similarity=0.549 Sum_probs=24.2
Q ss_pred CCceecCCCccccccchhHhhhhcccccc
Q 040287 73 PRTHECSVCGLEFAIGQALGGHMRRHRAV 101 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~~H~~~H~~~ 101 (162)
..|-.|..||.+|.......+||..|...
T Consensus 416 ~~pnqC~~CG~R~~~~ee~sk~md~H~dw 444 (579)
T KOG2071|consen 416 DSPNQCKSCGLRFDDSEERSKHMDIHDDW 444 (579)
T ss_pred CCcchhcccccccccchhhhhHhhhhhhh
Confidence 56789999999999998888888877443
No 129
>PF15269 zf-C2H2_7: Zinc-finger
Probab=47.54 E-value=9.8 Score=20.80 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=19.0
Q ss_pred ceecCCCccccccchhHhhhhcc
Q 040287 75 THECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
.|+|-.|..+...+++|-.||+-
T Consensus 20 ~ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred cceeecCCcccchHHHHHHHHHH
Confidence 36788888888889999999874
No 130
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=47.50 E-value=15 Score=32.39 Aligned_cols=19 Identities=26% Similarity=0.530 Sum_probs=13.2
Q ss_pred CccCCCCCCceecCCCccc
Q 040287 66 TQQSPAKPRTHECSVCGLE 84 (162)
Q Consensus 66 h~~~h~~~kp~~C~~C~k~ 84 (162)
|.--|....|..|+.||-.
T Consensus 466 H~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 466 HYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCCCCCCC
Confidence 3333446789999999854
No 131
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=47.15 E-value=8.6 Score=20.58 Aligned_cols=15 Identities=27% Similarity=0.755 Sum_probs=9.9
Q ss_pred CceecCCCccccccc
Q 040287 74 RTHECSVCGLEFAIG 88 (162)
Q Consensus 74 kp~~C~~C~k~F~~~ 88 (162)
-|+.|..|++.|=..
T Consensus 12 ~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLK 26 (43)
T ss_dssp SHEE-TTTS-EE-TT
T ss_pred CCeECCCCCcccCcc
Confidence 589999999999643
No 132
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=47.12 E-value=15 Score=20.58 Aligned_cols=14 Identities=43% Similarity=0.925 Sum_probs=9.7
Q ss_pred CceecCCCcccccc
Q 040287 74 RTHECSVCGLEFAI 87 (162)
Q Consensus 74 kp~~C~~C~k~F~~ 87 (162)
+.+.|..||+.|-.
T Consensus 17 rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 17 RRHHCRNCGRIFCS 30 (57)
T ss_pred cccccCcCcCCcCh
Confidence 45677788877754
No 133
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=46.80 E-value=21 Score=28.76 Aligned_cols=70 Identities=17% Similarity=0.163 Sum_probs=46.1
Q ss_pred ceeecCccCCccCChhHHHHHHHhcCCCCC----CC-CCCCCCcCccCCCCCCceecCCCc---cccccchhHhhhhcc
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASHKKPRL----TD-GTGGGADTQQSPAKPRTHECSVCG---LEFAIGQALGGHMRR 97 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~----~~-~~~~l~~h~~~h~~~kp~~C~~C~---k~F~~~~~L~~H~~~ 97 (162)
-|--|-.|++.+..-.....||..+++-.- |- ..-+|...+..- -..-|.|-.|+ +.|.+-...+.||..
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeK-V~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEK-VGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHH-hccCceEEEeccccCcccccHHHHHHHhh
Confidence 356789999999999988999988876321 11 000111110000 12357788888 999999999999974
No 134
>PRK12496 hypothetical protein; Provisional
Probab=46.37 E-value=17 Score=25.71 Aligned_cols=12 Identities=33% Similarity=0.988 Sum_probs=9.8
Q ss_pred eeecCccCCccC
Q 040287 28 VFECKTCNRQFP 39 (162)
Q Consensus 28 ~~~C~~C~k~f~ 39 (162)
.|.|..|++.|.
T Consensus 127 ~~~C~gC~~~~~ 138 (164)
T PRK12496 127 RKVCKGCKKKYP 138 (164)
T ss_pred eEECCCCCcccc
Confidence 388999998884
No 135
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=46.07 E-value=12 Score=30.87 Aligned_cols=29 Identities=17% Similarity=0.407 Sum_probs=24.1
Q ss_pred cCCCCCCceecCCCc-cccccchhHhhhhc
Q 040287 68 QSPAKPRTHECSVCG-LEFAIGQALGGHMR 96 (162)
Q Consensus 68 ~~h~~~kp~~C~~C~-k~F~~~~~L~~H~~ 96 (162)
+.|.-.+.|.|.+|| +++.....+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 345556789999999 99999999999954
No 136
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=44.22 E-value=19 Score=20.49 Aligned_cols=12 Identities=25% Similarity=0.952 Sum_probs=9.2
Q ss_pred eecCccCCccCC
Q 040287 29 FECKTCNRQFPS 40 (162)
Q Consensus 29 ~~C~~C~k~f~~ 40 (162)
.+|.+||+.|..
T Consensus 6 ~~C~~Cg~~~~~ 17 (54)
T PF14446_consen 6 CKCPVCGKKFKD 17 (54)
T ss_pred ccChhhCCcccC
Confidence 468899988853
No 137
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=43.33 E-value=16 Score=30.28 Aligned_cols=21 Identities=33% Similarity=0.678 Sum_probs=19.2
Q ss_pred eecCccCCccCChhHHHHHHH
Q 040287 29 FECKTCNRQFPSFQALGGHRA 49 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~ 49 (162)
+-|.+|+|+|++...|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 889999999999999998864
No 138
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=43.13 E-value=13 Score=29.63 Aligned_cols=29 Identities=31% Similarity=0.526 Sum_probs=24.2
Q ss_pred ceecCCCccccccchhHhhhhcc--cccccc
Q 040287 75 THECSVCGLEFAIGQALGGHMRR--HRAVAL 103 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~--H~~~~~ 103 (162)
.+.|-+|.+.|+.+..|+.|||. |....|
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 47899999999999999999985 554444
No 139
>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=43.04 E-value=11 Score=21.22 Aligned_cols=12 Identities=25% Similarity=0.675 Sum_probs=6.6
Q ss_pred ecCCCccccccc
Q 040287 77 ECSVCGLEFAIG 88 (162)
Q Consensus 77 ~C~~C~k~F~~~ 88 (162)
.|+.|++.|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 899999999743
No 140
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.89 E-value=5.7 Score=24.31 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=10.1
Q ss_pred eeecCccCCccC
Q 040287 28 VFECKTCNRQFP 39 (162)
Q Consensus 28 ~~~C~~C~k~f~ 39 (162)
.|+|..|+..|.
T Consensus 12 ~Y~c~~cg~~~d 23 (82)
T COG2331 12 SYECTECGNRFD 23 (82)
T ss_pred EEeecccchHHH
Confidence 599999998864
No 141
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=42.59 E-value=17 Score=25.04 Aligned_cols=22 Identities=18% Similarity=0.302 Sum_probs=16.3
Q ss_pred CCceecCCCccccccchhHhhh
Q 040287 73 PRTHECSVCGLEFAIGQALGGH 94 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~~H 94 (162)
+.=+.|+.||+.|=..++..+-
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CeEEECCCCCCEecccccHHHH
Confidence 3457899999999766666543
No 142
>PRK14873 primosome assembly protein PriA; Provisional
Probab=41.77 E-value=23 Score=30.87 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=8.7
Q ss_pred CceecCCCccc
Q 040287 74 RTHECSVCGLE 84 (162)
Q Consensus 74 kp~~C~~C~k~ 84 (162)
.|+.|+.||-.
T Consensus 421 ~p~~Cp~Cgs~ 431 (665)
T PRK14873 421 PDWRCPRCGSD 431 (665)
T ss_pred cCccCCCCcCC
Confidence 48899999854
No 143
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=40.20 E-value=13 Score=29.58 Aligned_cols=84 Identities=17% Similarity=0.179 Sum_probs=47.0
Q ss_pred CCCCCccccccccCCCc----eeecCccCCccCChhHHHHHHHhcCCCCCCCCCC-CCCcCc--------cCCCCCCcee
Q 040287 11 GGHFDAVNSVDMTAAGR----VFECKTCNRQFPSFQALGGHRASHKKPRLTDGTG-GGADTQ--------QSPAKPRTHE 77 (162)
Q Consensus 11 ~~~l~~~~h~~~h~~~k----~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~-~l~~h~--------~~h~~~kp~~ 77 (162)
+..|. .|...-..+. .-.|..|.+.|-....|.+|+|..+ ++-+.|.- +...|+ ..|-....|.
T Consensus 201 ~~~Lr--~H~~~G~~e~GFKGHP~C~FC~~~FYdDDEL~~HcR~~H-E~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ 277 (493)
T COG5236 201 SSTLR--DHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH-EACHICDMVGPIRYQYFKSYEDLEAHFRNAHYC 277 (493)
T ss_pred ccccc--ccccCCccccCcCCCchhhhccceecChHHHHHHHHhhh-hhhhhhhccCccchhhhhCHHHHHHHhhcCceE
Confidence 34455 5554433332 2468999999999999999988643 22222211 111111 1122233466
Q ss_pred cCC--C--c--cccccchhHhhhhcc
Q 040287 78 CSV--C--G--LEFAIGQALGGHMRR 97 (162)
Q Consensus 78 C~~--C--~--k~F~~~~~L~~H~~~ 97 (162)
|.+ | | ..|.....|..|+..
T Consensus 278 ct~qtc~~~k~~vf~~~~el~~h~~~ 303 (493)
T COG5236 278 CTFQTCRVGKCYVFPYHTELLEHLTR 303 (493)
T ss_pred EEEEEEecCcEEEeccHHHHHHHHHH
Confidence 654 3 2 578888889999754
No 144
>COG1773 Rubredoxin [Energy production and conversion]
Probab=39.15 E-value=16 Score=20.93 Aligned_cols=12 Identities=42% Similarity=1.041 Sum_probs=10.4
Q ss_pred ceecCCCccccc
Q 040287 75 THECSVCGLEFA 86 (162)
Q Consensus 75 p~~C~~C~k~F~ 86 (162)
.|+|..||..|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 589999999885
No 145
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=38.99 E-value=34 Score=19.22 Aligned_cols=42 Identities=24% Similarity=0.435 Sum_probs=23.7
Q ss_pred CceeecCc--cCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCC----Ccccccc
Q 040287 26 GRVFECKT--CNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSV----CGLEFAI 87 (162)
Q Consensus 26 ~k~~~C~~--C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~----C~k~F~~ 87 (162)
..+-.|+. |...+. ...|..|....- ..++..|++ |+..+..
T Consensus 7 ~~~v~C~~~cc~~~i~-r~~l~~H~~~~C-------------------~~~~v~C~~~~~GC~~~~~~ 54 (60)
T PF02176_consen 7 FRPVPCPNGCCNEMIP-RKELDDHLENEC-------------------PKRPVPCPYSPYGCKERVPR 54 (60)
T ss_dssp TSEEE-TT--S-BEEE-CCCHHHHHHTTS-------------------TTSEEE-SS----S--EEEH
T ss_pred CCEeeCCCCCccccee-HHHHHHHHHccC-------------------CCCcEECCCCCCCCCCccch
Confidence 45677877 545454 456888887432 345778888 8877753
No 146
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.81 E-value=33 Score=22.71 Aligned_cols=25 Identities=20% Similarity=0.327 Sum_probs=15.7
Q ss_pred ceeecCccCCccCChhHHHHHHHhc
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASH 51 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h 51 (162)
..|.|+.|...|-..-++-.|...|
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred cceeCCCCCCccccccchhhhhhcc
Confidence 3577777777776666655565544
No 147
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.68 E-value=25 Score=29.55 Aligned_cols=13 Identities=38% Similarity=0.948 Sum_probs=9.7
Q ss_pred CCCceecCCCccc
Q 040287 72 KPRTHECSVCGLE 84 (162)
Q Consensus 72 ~~kp~~C~~C~k~ 84 (162)
...|..|+.||-.
T Consensus 250 ~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 250 EPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCCCCCCC
Confidence 4558889999753
No 148
>PLN02294 cytochrome c oxidase subunit Vb
Probab=38.64 E-value=15 Score=26.17 Aligned_cols=22 Identities=23% Similarity=0.480 Sum_probs=17.1
Q ss_pred ccccccCCCceeecCccCCccCC
Q 040287 18 NSVDMTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 18 ~h~~~h~~~k~~~C~~C~k~f~~ 40 (162)
..+..+.+ ++++|.+||..|+-
T Consensus 132 ~Wf~L~kG-kp~RCpeCG~~fkL 153 (174)
T PLN02294 132 VWFWLEKG-KSFECPVCTQYFEL 153 (174)
T ss_pred EEEEecCC-CceeCCCCCCEEEE
Confidence 45566665 69999999999863
No 149
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=38.49 E-value=17 Score=23.61 Aligned_cols=16 Identities=38% Similarity=0.872 Sum_probs=13.2
Q ss_pred ceecCCCccccccchh
Q 040287 75 THECSVCGLEFAIGQA 90 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~ 90 (162)
|+.|..||..|...+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 6889999999988544
No 150
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=38.00 E-value=15 Score=30.49 Aligned_cols=22 Identities=27% Similarity=0.486 Sum_probs=19.7
Q ss_pred eecCCCccccccchhHhhhhcc
Q 040287 76 HECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
+.|.+|+++|.+...|..|..+
T Consensus 293 lyC~vCnKsFKseKq~kNHEnS 314 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHENS 314 (508)
T ss_pred eEEeeccccccchHHHHhhHHH
Confidence 7899999999999999999654
No 151
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=37.94 E-value=29 Score=18.93 Aligned_cols=14 Identities=36% Similarity=0.852 Sum_probs=11.0
Q ss_pred ceeecCccCCccCC
Q 040287 27 RVFECKTCNRQFPS 40 (162)
Q Consensus 27 k~~~C~~C~k~f~~ 40 (162)
..|.|+.||..+..
T Consensus 19 ~~~vC~~Cg~~~~~ 32 (52)
T smart00661 19 RRFVCRKCGYEEPI 32 (52)
T ss_pred CEEECCcCCCeEEC
Confidence 37999999987643
No 152
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=36.89 E-value=22 Score=28.37 Aligned_cols=23 Identities=22% Similarity=0.459 Sum_probs=21.3
Q ss_pred eeecCccCCccCChhHHHHHHHh
Q 040287 28 VFECKTCNRQFPSFQALGGHRAS 50 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~ 50 (162)
.+.|-.|.|.|+.+..|..|||.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 58999999999999999999975
No 154
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=36.73 E-value=25 Score=28.99 Aligned_cols=28 Identities=14% Similarity=0.400 Sum_probs=23.1
Q ss_pred ccCCCceeecCccC-CccCChhHHHHHHH
Q 040287 22 MTAAGRVFECKTCN-RQFPSFQALGGHRA 49 (162)
Q Consensus 22 ~h~~~k~~~C~~C~-k~f~~~~~L~~H~~ 49 (162)
.|-=...|.|.+|| +++.-...+.+|..
T Consensus 395 LHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 395 LHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hcCCCcccceeeccCccccCcHHHHHHhH
Confidence 44446779999999 99999999999974
No 155
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=36.70 E-value=54 Score=28.99 Aligned_cols=79 Identities=14% Similarity=0.063 Sum_probs=41.5
Q ss_pred hhhhhcCCCCCCccccccccCCCce--eecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCC
Q 040287 4 CLMFMSQGGHFDAVNSVDMTAAGRV--FECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVC 81 (162)
Q Consensus 4 C~k~f~~~~~l~~~~h~~~h~~~k~--~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C 81 (162)
|..+|.+...+. .++.+++..-+ +.|..|++.|.....-..++..+.-.. ..--.|.+|
T Consensus 294 ~St~p~~e~G~~--s~~~~psa~wpqhlP~g~~~~~~p~s~g~s~~a~~~Qv~~-----------------P~g~~~si~ 354 (907)
T KOG4167|consen 294 PSTIPLNEMGPQ--SQQLSPSAMWPQHLPDGRAQPGSPESSGQSKGAFGEQVDA-----------------PNGLTCSIC 354 (907)
T ss_pred cccchhhhcCCc--cccccchhhccccCcccccCCCCCCcccccccchHhhhcC-----------------CCCCccccc
Confidence 444555555555 66666665544 677777766654443333333221111 112346666
Q ss_pred ccccccchhHhhhhcccccc
Q 040287 82 GLEFAIGQALGGHMRRHRAV 101 (162)
Q Consensus 82 ~k~F~~~~~L~~H~~~H~~~ 101 (162)
++.|..-.....+++.+.+.
T Consensus 355 ~~~~~llP~a~~pI~aP~~~ 374 (907)
T KOG4167|consen 355 LKEFKLLPAANGPIRAPGGM 374 (907)
T ss_pred cCCCCcCcCCCCceecCCCC
Confidence 66666665555565555444
No 156
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=36.68 E-value=18 Score=19.51 Aligned_cols=15 Identities=33% Similarity=0.738 Sum_probs=11.7
Q ss_pred ecCCCccccccchhH
Q 040287 77 ECSVCGLEFAIGQAL 91 (162)
Q Consensus 77 ~C~~C~k~F~~~~~L 91 (162)
.|..||+.|+...-.
T Consensus 10 ~C~~C~rpf~WRKKW 24 (42)
T PF10013_consen 10 ICPVCGRPFTWRKKW 24 (42)
T ss_pred cCcccCCcchHHHHH
Confidence 499999999865443
No 157
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=36.65 E-value=25 Score=23.64 Aligned_cols=24 Identities=33% Similarity=0.521 Sum_probs=21.6
Q ss_pred ceeecCccCCccCChhHHHHHHHh
Q 040287 27 RVFECKTCNRQFPSFQALGGHRAS 50 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~ 50 (162)
..|-|-.|.+-|.....|..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 359999999999999999999875
No 158
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=36.30 E-value=18 Score=20.19 Aligned_cols=18 Identities=33% Similarity=0.722 Sum_probs=13.8
Q ss_pred CCceecCCCccccccchh
Q 040287 73 PRTHECSVCGLEFAIGQA 90 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~ 90 (162)
++.+.|..||..|.-...
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 467899999998875443
No 159
>PF14353 CpXC: CpXC protein
Probab=34.96 E-value=14 Score=24.73 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=18.4
Q ss_pred ceecCCCccccccchhHhhhhcc
Q 040287 75 THECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
.|.|+.||..|.-...+.-|-..
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCC
Confidence 58999999999877777766443
No 160
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.00 E-value=18 Score=21.14 Aligned_cols=19 Identities=5% Similarity=0.048 Sum_probs=14.0
Q ss_pred cccccCCCceeecCccCCc
Q 040287 19 SVDMTAAGRVFECKTCNRQ 37 (162)
Q Consensus 19 h~~~h~~~k~~~C~~C~k~ 37 (162)
|..++.+..++.|..-+-.
T Consensus 15 ~~~I~~~~~~l~C~g~~~p 33 (62)
T COG4391 15 HETIEIGDLPLMCPGPEPP 33 (62)
T ss_pred ceEEEeCCeeEEcCCCCCC
Confidence 6777888888888855544
No 161
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=32.78 E-value=21 Score=23.92 Aligned_cols=26 Identities=23% Similarity=0.349 Sum_probs=23.0
Q ss_pred CCCceecCCCccccccchhHhhhhcc
Q 040287 72 KPRTHECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
|--.|.|-.|.+-|.....|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 44569999999999999999999886
No 162
>PLN02748 tRNA dimethylallyltransferase
Probab=32.26 E-value=31 Score=28.76 Aligned_cols=24 Identities=13% Similarity=0.450 Sum_probs=20.8
Q ss_pred ceeecCccCC-ccCChhHHHHHHHh
Q 040287 27 RVFECKTCNR-QFPSFQALGGHRAS 50 (162)
Q Consensus 27 k~~~C~~C~k-~f~~~~~L~~H~~~ 50 (162)
+.|.|++|++ ++.....+..|.+.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 6799999997 89999999999854
No 163
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=32.22 E-value=29 Score=16.78 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=5.0
Q ss_pred CceecCCCcccc
Q 040287 74 RTHECSVCGLEF 85 (162)
Q Consensus 74 kp~~C~~C~k~F 85 (162)
-.|.|..|+..+
T Consensus 14 ~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 14 WFYRCSECDFDL 25 (30)
T ss_dssp -EEE-TTT----
T ss_pred ceEECccCCCcc
Confidence 478888887543
No 164
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=32.14 E-value=27 Score=24.25 Aligned_cols=17 Identities=18% Similarity=0.516 Sum_probs=12.3
Q ss_pred cccCCCce----eecCccCCc
Q 040287 21 DMTAAGRV----FECKTCNRQ 37 (162)
Q Consensus 21 ~~h~~~k~----~~C~~C~k~ 37 (162)
..++||++ |.|..||..
T Consensus 101 ~Y~sGE~~g~G~l~C~~Cg~~ 121 (146)
T PF07295_consen 101 VYHSGEVVGPGTLVCENCGHE 121 (146)
T ss_pred CeecCcEecCceEecccCCCE
Confidence 45667654 899999865
No 165
>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=32.08 E-value=37 Score=17.22 Aligned_cols=21 Identities=29% Similarity=0.596 Sum_probs=13.6
Q ss_pred ceecCCCccccccchhHhhhhc
Q 040287 75 THECSVCGLEFAIGQALGGHMR 96 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~ 96 (162)
-+.|+.|++.+. .+.+..|+.
T Consensus 4 ~~~C~nC~R~v~-a~RfA~HLe 24 (33)
T PF08209_consen 4 YVECPNCGRPVA-ASRFAPHLE 24 (33)
T ss_dssp EEE-TTTSSEEE-GGGHHHHHH
T ss_pred eEECCCCcCCcc-hhhhHHHHH
Confidence 478999999876 444555544
No 166
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=31.61 E-value=25 Score=28.15 Aligned_cols=28 Identities=18% Similarity=0.398 Sum_probs=22.7
Q ss_pred CCCCCCceecCCCc-cccccchhHhhhhc
Q 040287 69 SPAKPRTHECSVCG-LEFAIGQALGGHMR 96 (162)
Q Consensus 69 ~h~~~kp~~C~~C~-k~F~~~~~L~~H~~ 96 (162)
.|.-.+-|.|.+|| +++.....+.+|..
T Consensus 368 lhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 368 LHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred hcCCCcceeeeecccccccchHHHHhhhh
Confidence 45556779999999 88888889988854
No 167
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=30.83 E-value=11 Score=21.70 Aligned_cols=26 Identities=15% Similarity=0.235 Sum_probs=15.2
Q ss_pred cchhhhhcCCCCCCccccccccCCCceeecCccCCcc
Q 040287 2 ANCLMFMSQGGHFDAVNSVDMTAAGRVFECKTCNRQF 38 (162)
Q Consensus 2 a~C~k~f~~~~~l~~~~h~~~h~~~k~~~C~~C~k~f 38 (162)
|.||+.|--.+.-. +-=.|+.|.+.|
T Consensus 29 ALCGk~wvp~rdp~-----------~~PVCP~Ck~iy 54 (58)
T PF11238_consen 29 ALCGKVWVPTRDPK-----------PFPVCPECKEIY 54 (58)
T ss_pred eeeCceeCCCCCCC-----------CCCCCcCHHHHH
Confidence 77888885543332 233577776554
No 168
>PRK04351 hypothetical protein; Provisional
Probab=30.48 E-value=34 Score=23.84 Aligned_cols=17 Identities=12% Similarity=0.374 Sum_probs=12.1
Q ss_pred CCCceecCCCccccccc
Q 040287 72 KPRTHECSVCGLEFAIG 88 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~ 88 (162)
+...|.|..|+-.+...
T Consensus 129 n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 129 NTKRYRCGKCRGKLKLI 145 (149)
T ss_pred CCCcEEeCCCCcEeeec
Confidence 34679999998766543
No 169
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=30.45 E-value=25 Score=19.76 Aligned_cols=26 Identities=23% Similarity=0.318 Sum_probs=15.7
Q ss_pred CceecCCCccccccchhHhhhhcccc
Q 040287 74 RTHECSVCGLEFAIGQALGGHMRRHR 99 (162)
Q Consensus 74 kp~~C~~C~k~F~~~~~L~~H~~~H~ 99 (162)
..|.|+.|+..|-..=..-.|...|.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS-S
T ss_pred CeEECCCCCCccccCcChhhhccccC
Confidence 47999999999987777777776664
No 170
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=30.31 E-value=27 Score=18.13 Aligned_cols=13 Identities=23% Similarity=0.928 Sum_probs=7.5
Q ss_pred CceeecCccCCcc
Q 040287 26 GRVFECKTCNRQF 38 (162)
Q Consensus 26 ~k~~~C~~C~k~f 38 (162)
.+.|+|..||...
T Consensus 4 ~~~YkC~~CGniV 16 (36)
T PF06397_consen 4 GEFYKCEHCGNIV 16 (36)
T ss_dssp TEEEE-TTT--EE
T ss_pred ccEEEccCCCCEE
Confidence 3579999999764
No 171
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.22 E-value=30 Score=23.24 Aligned_cols=23 Identities=13% Similarity=0.118 Sum_probs=16.0
Q ss_pred ccccccCCCceeecCccCCccCCh
Q 040287 18 NSVDMTAAGRVFECKTCNRQFPSF 41 (162)
Q Consensus 18 ~h~~~h~~~k~~~C~~C~k~f~~~ 41 (162)
.-..+..-.-.+.| .||..|...
T Consensus 60 A~L~I~~vp~~~~C-~Cg~~~~~~ 82 (124)
T PRK00762 60 ADLIVEMIPVEIEC-ECGYEGVVD 82 (124)
T ss_pred CEEEEEecCeeEEe-eCcCccccc
Confidence 44445556667999 999887643
No 172
>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=30.13 E-value=27 Score=29.10 Aligned_cols=30 Identities=27% Similarity=0.347 Sum_probs=24.9
Q ss_pred CCceecCCCccccccchhHhhhhc-cccccc
Q 040287 73 PRTHECSVCGLEFAIGQALGGHMR-RHRAVA 102 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~~H~~-~H~~~~ 102 (162)
-+=+.|+.|.+.|.....+..|+. .|.+.-
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 345789999999999999999988 476553
No 173
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=30.01 E-value=17 Score=26.54 Aligned_cols=27 Identities=19% Similarity=0.450 Sum_probs=0.0
Q ss_pred CCCCCceecCCCc-cccccchhHhhhhc
Q 040287 70 PAKPRTHECSVCG-LEFAIGQALGGHMR 96 (162)
Q Consensus 70 h~~~kp~~C~~C~-k~F~~~~~L~~H~~ 96 (162)
|.-.+-|.|.+|| .+|.....+.+|-.
T Consensus 96 hGL~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 96 HGLGVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp ----------------------------
T ss_pred hCCCCeeeeEeCCCcceecHHHHHHhcC
Confidence 3345679999997 56777788888854
No 174
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.92 E-value=26 Score=23.78 Aligned_cols=17 Identities=24% Similarity=0.677 Sum_probs=13.8
Q ss_pred CCCceecCCCccccccc
Q 040287 72 KPRTHECSVCGLEFAIG 88 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~~~ 88 (162)
|...|.|+.|+++|...
T Consensus 50 ~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 50 GHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cccccccCCcCcceeee
Confidence 46679999999999743
No 175
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=28.93 E-value=39 Score=28.03 Aligned_cols=13 Identities=31% Similarity=0.843 Sum_probs=10.5
Q ss_pred ceeecCccCCccC
Q 040287 27 RVFECKTCNRQFP 39 (162)
Q Consensus 27 k~~~C~~C~k~f~ 39 (162)
..|.|..||..+.
T Consensus 6 ~~y~C~~Cg~~~~ 18 (454)
T TIGR00416 6 SKFVCQHCGADSP 18 (454)
T ss_pred CeEECCcCCCCCc
Confidence 3599999998764
No 176
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=28.89 E-value=22 Score=19.87 Aligned_cols=12 Identities=25% Similarity=0.980 Sum_probs=10.1
Q ss_pred eecCccCCccCC
Q 040287 29 FECKTCNRQFPS 40 (162)
Q Consensus 29 ~~C~~C~k~f~~ 40 (162)
|+|.+||..|..
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 789999998864
No 177
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=28.87 E-value=36 Score=29.08 Aligned_cols=27 Identities=22% Similarity=0.430 Sum_probs=21.3
Q ss_pred CCceeecCccCCccCChhHHHHHHHhc
Q 040287 25 AGRVFECKTCNRQFPSFQALGGHRASH 51 (162)
Q Consensus 25 ~~k~~~C~~C~k~f~~~~~L~~H~~~h 51 (162)
..++-.|..||.+|........|+..|
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H 441 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIH 441 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhh
Confidence 456799999999999887777666555
No 178
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=28.70 E-value=21 Score=25.02 Aligned_cols=21 Identities=10% Similarity=0.175 Sum_probs=11.6
Q ss_pred chhhhhcCCCCCCcccccccc
Q 040287 3 NCLMFMSQGGHFDAVNSVDMT 23 (162)
Q Consensus 3 ~C~k~f~~~~~l~~~~h~~~h 23 (162)
.|+|.|.+++.-....|+-.|
T Consensus 19 ~c~kWFCNg~~~~s~SHIv~H 39 (152)
T PF09416_consen 19 TCNKWFCNGRGNTSGSHIVNH 39 (152)
T ss_dssp TTTEEEES--TTSSS-HHHHH
T ss_pred CCCcEeecCCCCCcccHHHHH
Confidence 477888887766555665433
No 179
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=28.15 E-value=40 Score=29.43 Aligned_cols=24 Identities=25% Similarity=0.314 Sum_probs=15.5
Q ss_pred eecCccCCccCChhHHHHHHHhcC
Q 040287 29 FECKTCNRQFPSFQALGGHRASHK 52 (162)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~H~~~h~ 52 (162)
-.|..|...|-....|.+|++.++
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h 206 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDH 206 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccce
Confidence 356667777777777777766543
No 180
>PTZ00448 hypothetical protein; Provisional
Probab=28.01 E-value=30 Score=27.84 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=21.2
Q ss_pred ceecCCCccccccchhHhhhhcc
Q 040287 75 THECSVCGLEFAIGQALGGHMRR 97 (162)
Q Consensus 75 p~~C~~C~k~F~~~~~L~~H~~~ 97 (162)
.|.|..|+-.|......+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999989999999987
No 181
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=27.83 E-value=37 Score=23.25 Aligned_cols=13 Identities=23% Similarity=0.618 Sum_probs=9.8
Q ss_pred CceecCCCccccc
Q 040287 74 RTHECSVCGLEFA 86 (162)
Q Consensus 74 kp~~C~~C~k~F~ 86 (162)
.-|.|..|+-.+.
T Consensus 132 ~~y~C~~C~g~l~ 144 (146)
T smart00731 132 SRYRCGKCGGKLI 144 (146)
T ss_pred ceEEcCCCCCEEE
Confidence 5689999987653
No 182
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=27.82 E-value=30 Score=19.03 Aligned_cols=14 Identities=14% Similarity=0.607 Sum_probs=10.9
Q ss_pred eeecCccCCccCCh
Q 040287 28 VFECKTCNRQFPSF 41 (162)
Q Consensus 28 ~~~C~~C~k~f~~~ 41 (162)
.|+|.+|+..|...
T Consensus 1 ky~C~~CgyvYd~~ 14 (47)
T PF00301_consen 1 KYQCPVCGYVYDPE 14 (47)
T ss_dssp EEEETTTSBEEETT
T ss_pred CcCCCCCCEEEcCC
Confidence 38899999888643
No 183
>PRK06260 threonine synthase; Validated
Probab=27.81 E-value=45 Score=26.94 Aligned_cols=11 Identities=18% Similarity=1.005 Sum_probs=9.4
Q ss_pred eecCccCCccC
Q 040287 29 FECKTCNRQFP 39 (162)
Q Consensus 29 ~~C~~C~k~f~ 39 (162)
++|..||+.|.
T Consensus 4 ~~C~~cg~~~~ 14 (397)
T PRK06260 4 LKCIECGKEYD 14 (397)
T ss_pred EEECCCCCCCC
Confidence 78999998875
No 184
>PRK11823 DNA repair protein RadA; Provisional
Probab=27.52 E-value=46 Score=27.47 Aligned_cols=14 Identities=21% Similarity=0.778 Sum_probs=11.0
Q ss_pred CceeecCccCCccC
Q 040287 26 GRVFECKTCNRQFP 39 (162)
Q Consensus 26 ~k~~~C~~C~k~f~ 39 (162)
+..|.|..||..+.
T Consensus 5 ~~~y~C~~Cg~~~~ 18 (446)
T PRK11823 5 KTAYVCQECGAESP 18 (446)
T ss_pred CCeEECCcCCCCCc
Confidence 34699999998764
No 185
>PRK05580 primosome assembly protein PriA; Validated
Probab=26.72 E-value=50 Score=28.90 Aligned_cols=13 Identities=31% Similarity=0.846 Sum_probs=9.8
Q ss_pred CCCceecCCCccc
Q 040287 72 KPRTHECSVCGLE 84 (162)
Q Consensus 72 ~~kp~~C~~C~k~ 84 (162)
...|..|+.||..
T Consensus 418 ~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 418 EPIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCCcCC
Confidence 4567889999754
No 186
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=26.66 E-value=27 Score=24.22 Aligned_cols=24 Identities=21% Similarity=0.445 Sum_probs=18.9
Q ss_pred CCceecCCCccccccchhHhhhhc
Q 040287 73 PRTHECSVCGLEFAIGQALGGHMR 96 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~~H~~ 96 (162)
.-+|.|.-||-.+-...-+..|..
T Consensus 127 ~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 127 DSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CchhHHHhcCCceeechhhhhccc
Confidence 447889999998888888877754
No 187
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=26.05 E-value=36 Score=23.31 Aligned_cols=13 Identities=23% Similarity=0.664 Sum_probs=9.8
Q ss_pred CceecCCCccccc
Q 040287 74 RTHECSVCGLEFA 86 (162)
Q Consensus 74 kp~~C~~C~k~F~ 86 (162)
+.|.|..|+..|.
T Consensus 142 ~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 142 KRYRCGRCGGPLV 154 (157)
T ss_pred hhEECCCCCCEEE
Confidence 3489999987664
No 188
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=25.94 E-value=23 Score=24.28 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=17.1
Q ss_pred ccccccCCCceeecCccCCccCC
Q 040287 18 NSVDMTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 18 ~h~~~h~~~k~~~C~~C~k~f~~ 40 (162)
..+..+.+ ++.+|..||..|.-
T Consensus 103 ~W~~l~~g-~~~RCpeCG~~fkL 124 (136)
T PF01215_consen 103 IWFWLHKG-KPQRCPECGQVFKL 124 (136)
T ss_dssp EEEEEETT-SEEEETTTEEEEEE
T ss_pred EEEEEeCC-CccCCCCCCeEEEE
Confidence 45667766 58999999999864
No 189
>PLN02748 tRNA dimethylallyltransferase
Probab=24.10 E-value=43 Score=27.98 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=22.1
Q ss_pred CCceecCCCcc-ccccchhHhhhhccc
Q 040287 73 PRTHECSVCGL-EFAIGQALGGHMRRH 98 (162)
Q Consensus 73 ~kp~~C~~C~k-~F~~~~~L~~H~~~H 98 (162)
.+.|.|+.|++ .+........|++..
T Consensus 416 ~~~~~Ce~C~~~~~~G~~eW~~Hlksr 442 (468)
T PLN02748 416 WTQYVCEACGNKVLRGAHEWEQHKQGR 442 (468)
T ss_pred cccccccCCCCcccCCHHHHHHHhcch
Confidence 47789999997 899999999998753
No 190
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.82 E-value=25 Score=19.53 Aligned_cols=15 Identities=27% Similarity=0.581 Sum_probs=11.5
Q ss_pred ecCCCccccccchhH
Q 040287 77 ECSVCGLEFAIGQAL 91 (162)
Q Consensus 77 ~C~~C~k~F~~~~~L 91 (162)
-|++|++.|+.....
T Consensus 14 ICpvCqRPFsWRkKW 28 (54)
T COG4338 14 ICPVCQRPFSWRKKW 28 (54)
T ss_pred hhhhhcCchHHHHHH
Confidence 499999999865443
No 191
>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=23.77 E-value=48 Score=16.39 Aligned_cols=12 Identities=33% Similarity=0.653 Sum_probs=8.6
Q ss_pred CCceecCCCccc
Q 040287 73 PRTHECSVCGLE 84 (162)
Q Consensus 73 ~kp~~C~~C~k~ 84 (162)
...|.|+.|+..
T Consensus 17 ~~~~vCp~C~~e 28 (30)
T PF08274_consen 17 GELLVCPECGHE 28 (30)
T ss_dssp SSSEEETTTTEE
T ss_pred CCEEeCCccccc
Confidence 446889988754
No 192
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=23.48 E-value=1.2e+02 Score=24.09 Aligned_cols=72 Identities=15% Similarity=0.112 Sum_probs=40.7
Q ss_pred ceeecCccCCccCChhHHHHHHHhcCCCCCCCCCC----CCCcCccC----CCCCCceecCCCccccccchhHhhhhccc
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTG----GGADTQQS----PAKPRTHECSVCGLEFAIGQALGGHMRRH 98 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~----~l~~h~~~----h~~~kp~~C~~C~k~F~~~~~L~~H~~~H 98 (162)
-|-.|++|+-+.-...+|.+-.+.--.-++|.... ....+-.. -.+.-.|.|..|.-.|-..-+.-.|...|
T Consensus 289 LP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccceeeccchHHHHhhhh
Confidence 36677888888877777776433222222332000 00111111 12334699999999998777777776655
No 193
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=23.17 E-value=42 Score=17.15 Aligned_cols=14 Identities=29% Similarity=0.641 Sum_probs=7.3
Q ss_pred eecCCCccccccch
Q 040287 76 HECSVCGLEFAIGQ 89 (162)
Q Consensus 76 ~~C~~C~k~F~~~~ 89 (162)
-.|..|++.|..+-
T Consensus 4 ~~C~eC~~~f~dSy 17 (34)
T PF01286_consen 4 PKCDECGKPFMDSY 17 (34)
T ss_dssp EE-TTT--EES-SS
T ss_pred chHhHhCCHHHHHH
Confidence 36999999997543
No 194
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=23.11 E-value=45 Score=18.78 Aligned_cols=19 Identities=16% Similarity=0.448 Sum_probs=13.2
Q ss_pred ccCCCceeecCccCCccCC
Q 040287 22 MTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 22 ~h~~~k~~~C~~C~k~f~~ 40 (162)
+..+...|+|..|++.+..
T Consensus 29 ~~~~~~~~rC~YCe~~~~~ 47 (52)
T PF02748_consen 29 IDKEPIKLRCHYCERIITE 47 (52)
T ss_dssp EETTTCEEEETTT--EEEH
T ss_pred EeCCCCEEEeeCCCCEecc
Confidence 4556778999999998764
No 195
>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=22.90 E-value=38 Score=19.26 Aligned_cols=13 Identities=38% Similarity=0.922 Sum_probs=10.0
Q ss_pred eecCCCccccccc
Q 040287 76 HECSVCGLEFAIG 88 (162)
Q Consensus 76 ~~C~~C~k~F~~~ 88 (162)
++|+.||..+.-.
T Consensus 3 ~~CP~CG~~iev~ 15 (54)
T TIGR01206 3 FECPDCGAEIELE 15 (54)
T ss_pred cCCCCCCCEEecC
Confidence 6899999877543
No 196
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.14 E-value=31 Score=25.95 Aligned_cols=27 Identities=30% Similarity=0.541 Sum_probs=18.7
Q ss_pred CCceecCCCccccccchhHhhhhcccc
Q 040287 73 PRTHECSVCGLEFAIGQALGGHMRRHR 99 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~~H~~~H~ 99 (162)
++.+.|++|+..|....-+..-.|+-.
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiia 43 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIA 43 (267)
T ss_pred hceeccCcccchhhhhheeccceeEec
Confidence 567899999999976655444444433
No 197
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=22.14 E-value=46 Score=25.46 Aligned_cols=13 Identities=31% Similarity=0.677 Sum_probs=10.1
Q ss_pred CCceecCCCcccc
Q 040287 73 PRTHECSVCGLEF 85 (162)
Q Consensus 73 ~kp~~C~~C~k~F 85 (162)
.+.|.|++||-+=
T Consensus 266 LR~YVCPiCGATg 278 (318)
T KOG4602|consen 266 LRSYVCPICGATG 278 (318)
T ss_pred HhhhcCccccccC
Confidence 4679999998653
No 198
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=21.68 E-value=35 Score=21.30 Aligned_cols=16 Identities=25% Similarity=0.395 Sum_probs=12.0
Q ss_pred CCceecCCCccccccc
Q 040287 73 PRTHECSVCGLEFAIG 88 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~ 88 (162)
.-.|.|..|.+.|...
T Consensus 52 vGiW~C~~C~kv~agg 67 (92)
T KOG0402|consen 52 VGIWKCGSCKKVVAGG 67 (92)
T ss_pred eeEEecCCccceeccc
Confidence 3468899998888644
No 199
>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=21.43 E-value=31 Score=25.59 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=0.0
Q ss_pred CCceecCCCccccccchhHhhhhccccccccC
Q 040287 73 PRTHECSVCGLEFAIGQALGGHMRRHRAVALH 104 (162)
Q Consensus 73 ~kp~~C~~C~k~F~~~~~L~~H~~~H~~~~~~ 104 (162)
.+-..|++||.... .+.+..|||+..-...+
T Consensus 166 ~~~~~cPitGe~IP-~~e~~eHmRi~LlDP~w 196 (229)
T PF12230_consen 166 EKMIICPITGEMIP-ADEMDEHMRIELLDPRW 196 (229)
T ss_dssp --------------------------------
T ss_pred cccccccccccccc-ccccccccccccccccc
Confidence 44578999999887 67899999987655443
No 200
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=21.24 E-value=49 Score=17.03 Aligned_cols=11 Identities=27% Similarity=0.776 Sum_probs=8.5
Q ss_pred eecCCCccccc
Q 040287 76 HECSVCGLEFA 86 (162)
Q Consensus 76 ~~C~~C~k~F~ 86 (162)
+.|+.||+.|.
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 46888988874
No 201
>PTZ00448 hypothetical protein; Provisional
Probab=21.21 E-value=67 Score=25.93 Aligned_cols=23 Identities=30% Similarity=0.573 Sum_probs=19.9
Q ss_pred eeecCccCCccCChhHHHHHHHh
Q 040287 28 VFECKTCNRQFPSFQALGGHRAS 50 (162)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~H~~~ 50 (162)
.|.|..|+-.|......+.|+++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999888888888875
No 202
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=20.98 E-value=42 Score=25.20 Aligned_cols=20 Identities=20% Similarity=0.592 Sum_probs=15.0
Q ss_pred ccccCCCceeecCccCCccCC
Q 040287 20 VDMTAAGRVFECKTCNRQFPS 40 (162)
Q Consensus 20 ~~~h~~~k~~~C~~C~k~f~~ 40 (162)
+..+. .++.+|.+||..|.-
T Consensus 174 FwLrE-GkpqRCpECGqVFKL 193 (268)
T PTZ00043 174 FRCRE-GFLYRCGECDQIFML 193 (268)
T ss_pred EEecC-CCCccCCCCCcEEEE
Confidence 33444 469999999999974
No 203
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=20.56 E-value=58 Score=18.65 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=12.0
Q ss_pred CCCceecCCCccccc
Q 040287 72 KPRTHECSVCGLEFA 86 (162)
Q Consensus 72 ~~kp~~C~~C~k~F~ 86 (162)
+...|.|+.||..+-
T Consensus 11 ~~v~~~Cp~cGipth 25 (55)
T PF13824_consen 11 AHVNFECPDCGIPTH 25 (55)
T ss_pred cccCCcCCCCCCcCc
Confidence 456899999998764
No 204
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=20.54 E-value=43 Score=23.29 Aligned_cols=19 Identities=26% Similarity=0.436 Sum_probs=14.4
Q ss_pred CceecCCCccccccchhHh
Q 040287 74 RTHECSVCGLEFAIGQALG 92 (162)
Q Consensus 74 kp~~C~~C~k~F~~~~~L~ 92 (162)
+.-+|..||+.|++-....
T Consensus 27 RRReC~~C~~RFTTyErve 45 (147)
T TIGR00244 27 RRRECLECHERFTTFERAE 45 (147)
T ss_pred ecccCCccCCccceeeecc
Confidence 4468999999998765443
No 205
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.50 E-value=57 Score=23.46 Aligned_cols=17 Identities=12% Similarity=0.483 Sum_probs=10.7
Q ss_pred CCceeecCccCCccCCh
Q 040287 25 AGRVFECKTCNRQFPSF 41 (162)
Q Consensus 25 ~~k~~~C~~C~k~f~~~ 41 (162)
...-|.|+.|.-.|+..
T Consensus 110 ~~~~y~C~~~~~r~sfd 126 (176)
T COG1675 110 ENNYYVCPNCHVKYSFD 126 (176)
T ss_pred cCCceeCCCCCCcccHH
Confidence 34568887777666543
No 206
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=20.49 E-value=54 Score=17.01 Aligned_cols=16 Identities=25% Similarity=0.511 Sum_probs=9.6
Q ss_pred eecCCCccccccchhH
Q 040287 76 HECSVCGLEFAIGQAL 91 (162)
Q Consensus 76 ~~C~~C~k~F~~~~~L 91 (162)
-.|+.|++.|-+.+..
T Consensus 3 ~~CprC~kg~Hwa~~C 18 (36)
T PF14787_consen 3 GLCPRCGKGFHWASEC 18 (36)
T ss_dssp -C-TTTSSSCS-TTT-
T ss_pred ccCcccCCCcchhhhh
Confidence 4588999998766654
No 207
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=20.39 E-value=30 Score=18.21 Aligned_cols=14 Identities=29% Similarity=0.605 Sum_probs=5.6
Q ss_pred cCCCccccccchhH
Q 040287 78 CSVCGLEFAIGQAL 91 (162)
Q Consensus 78 C~~C~k~F~~~~~L 91 (162)
|.+|++.|.....+
T Consensus 1 C~~C~~~~~~~~~~ 14 (47)
T PF01844_consen 1 CQYCGKPGSDNESL 14 (47)
T ss_dssp -TTT--B--GG-GE
T ss_pred CCCCCCcCccCcce
Confidence 78899888766333
No 208
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=20.34 E-value=61 Score=26.15 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=7.8
Q ss_pred eecCccCCccC
Q 040287 29 FECKTCNRQFP 39 (162)
Q Consensus 29 ~~C~~C~k~f~ 39 (162)
|.|..||..+.
T Consensus 1 ~~c~~cg~~~~ 11 (372)
T cd01121 1 YVCSECGYVSP 11 (372)
T ss_pred CCCCCCCCCCC
Confidence 67888887653
No 209
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=20.18 E-value=1.8e+02 Score=18.79 Aligned_cols=38 Identities=16% Similarity=0.245 Sum_probs=28.5
Q ss_pred ceeecCccCCccCChhHHHHHHHhcCCCCCCCCCCCCCcCccCCCCCCceecCCCccc
Q 040287 27 RVFECKTCNRQFPSFQALGGHRASHKKPRLTDGTGGGADTQQSPAKPRTHECSVCGLE 84 (162)
Q Consensus 27 k~~~C~~C~k~f~~~~~L~~H~~~h~~~~~~~~~~~l~~h~~~h~~~kp~~C~~C~k~ 84 (162)
..|.|+.-|..|......-..+..- ..+-|.|...|++
T Consensus 2 eVf~i~~T~EiF~dYe~Y~~R~~~y--------------------~~~vwtC~~TGk~ 39 (102)
T PF10537_consen 2 EVFYIPFTGEIFRDYEEYLKRMILY--------------------NQRVWTCEITGKS 39 (102)
T ss_pred ceEEeCCCCcccCCHHHHHHHHHHH--------------------hCCeeEEecCCCC
Confidence 4688888899998887776666544 4567999988763
No 210
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=20.13 E-value=67 Score=16.69 Aligned_cols=22 Identities=18% Similarity=0.240 Sum_probs=9.3
Q ss_pred ceecCCCccccccch--hHhhhhc
Q 040287 75 THECSVCGLEFAIGQ--ALGGHMR 96 (162)
Q Consensus 75 p~~C~~C~k~F~~~~--~L~~H~~ 96 (162)
.|-|++|..-|...+ ..+.|.+
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT-
T ss_pred CeecccccceecCCChHHHHHhhc
Confidence 478999999995433 4466654
Done!