Query 041414
Match_columns 152
No_of_seqs 219 out of 1557
Neff 10.0
Searched_HMMs 46136
Date Fri Mar 29 06:47:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041414.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041414hhsearch_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 7.5E-26 1.6E-30 157.8 4.2 124 2-129 134-270 (279)
2 KOG2462 C2H2-type Zn-finger pr 99.8 3.1E-22 6.7E-27 139.8 1.1 92 2-97 165-265 (279)
3 KOG1074 Transcriptional repres 99.7 4.1E-18 8.8E-23 133.7 1.0 48 3-52 358-405 (958)
4 KOG3576 Ovo and related transc 99.5 1.5E-15 3.2E-20 102.3 -2.3 74 24-97 113-195 (267)
5 KOG3623 Homeobox transcription 99.4 1.1E-14 2.3E-19 113.5 0.1 73 24-96 890-971 (1007)
6 KOG1074 Transcriptional repres 99.4 1.6E-14 3.6E-19 113.8 -0.3 82 2-100 609-693 (958)
7 KOG3623 Homeobox transcription 99.4 1.2E-13 2.6E-18 107.8 1.5 70 54-123 892-971 (1007)
8 KOG3608 Zn finger proteins [Ge 99.4 2.7E-14 5.8E-19 103.3 -3.0 135 2-145 183-358 (467)
9 KOG3576 Ovo and related transc 99.3 1.2E-13 2.5E-18 93.2 -0.3 75 52-126 113-197 (267)
10 PHA00733 hypothetical protein 99.2 1.6E-11 3.6E-16 78.9 4.2 76 3-100 45-124 (128)
11 KOG3608 Zn finger proteins [Ge 99.1 2.2E-11 4.8E-16 88.4 2.2 93 2-97 267-374 (467)
12 PHA02768 hypothetical protein; 99.1 6.4E-11 1.4E-15 64.0 2.0 44 28-92 5-48 (55)
13 PLN03086 PRLI-interacting fact 98.9 3.6E-09 7.8E-14 82.5 6.1 83 28-115 453-554 (567)
14 PHA02768 hypothetical protein; 98.8 3.9E-09 8.5E-14 57.1 2.4 42 75-118 5-47 (55)
15 PF13465 zf-H2C2_2: Zinc-finge 98.8 7.4E-10 1.6E-14 51.4 -0.5 23 17-39 3-25 (26)
16 PF13465 zf-H2C2_2: Zinc-finge 98.7 9.1E-09 2E-13 47.7 2.3 26 43-87 1-26 (26)
17 PHA00733 hypothetical protein 98.7 6E-09 1.3E-13 67.1 0.5 87 25-126 37-123 (128)
18 PHA00732 hypothetical protein 98.6 3.3E-08 7.1E-13 58.2 2.7 47 28-99 1-48 (79)
19 PHA00616 hypothetical protein 98.6 2.9E-08 6.4E-13 51.1 1.4 31 75-105 1-31 (44)
20 PLN03086 PRLI-interacting fact 98.5 9.4E-08 2E-12 74.8 3.1 86 3-97 458-562 (567)
21 PHA00616 hypothetical protein 98.5 5.9E-08 1.3E-12 50.0 1.3 32 28-59 1-32 (44)
22 KOG3993 Transcription factor ( 98.4 7.6E-08 1.7E-12 71.8 1.5 75 27-101 294-382 (500)
23 PF00096 zf-C2H2: Zinc finger, 98.3 3.1E-07 6.8E-12 41.1 1.7 23 76-98 1-23 (23)
24 COG5189 SFP1 Putative transcri 98.2 6.4E-07 1.4E-11 64.8 2.6 72 24-96 345-419 (423)
25 KOG3993 Transcription factor ( 98.1 1.8E-06 3.9E-11 64.6 2.9 50 2-53 299-381 (500)
26 PF00096 zf-C2H2: Zinc finger, 98.1 1.7E-06 3.7E-11 38.6 1.6 23 29-51 1-23 (23)
27 PF05605 zf-Di19: Drought indu 98.1 6.4E-06 1.4E-10 45.0 4.2 51 28-99 2-53 (54)
28 PF13912 zf-C2H2_6: C2H2-type 98.0 4E-06 8.6E-11 39.0 1.6 26 75-100 1-26 (27)
29 PF13894 zf-C2H2_4: C2H2-type 98.0 5.1E-06 1.1E-10 37.2 1.8 24 76-99 1-24 (24)
30 PHA00732 hypothetical protein 97.9 8.3E-06 1.8E-10 48.0 2.2 38 75-114 1-39 (79)
31 PF12756 zf-C2H2_2: C2H2 type 97.7 2.3E-05 5E-10 47.9 2.6 70 30-100 1-75 (100)
32 PF13912 zf-C2H2_6: C2H2-type 97.7 1.8E-05 3.9E-10 36.7 1.3 25 28-52 1-25 (27)
33 PF13894 zf-C2H2_4: C2H2-type 97.7 3.3E-05 7E-10 34.4 2.0 23 29-51 1-23 (24)
34 PF09237 GAGA: GAGA factor; I 97.7 4.1E-05 8.8E-10 40.5 2.5 32 72-103 21-52 (54)
35 smart00355 ZnF_C2H2 zinc finge 97.6 5.6E-05 1.2E-09 34.2 1.8 25 76-100 1-25 (26)
36 PF09237 GAGA: GAGA factor; I 97.5 0.00013 2.7E-09 38.6 2.6 33 24-56 20-52 (54)
37 smart00355 ZnF_C2H2 zinc finge 97.3 0.00025 5.5E-09 31.9 2.1 24 29-52 1-24 (26)
38 PF12874 zf-met: Zinc-finger o 97.1 0.00034 7.3E-09 31.6 1.4 23 76-98 1-23 (25)
39 PRK04860 hypothetical protein; 96.8 0.00084 1.8E-08 44.9 2.2 39 27-88 118-156 (160)
40 PF13909 zf-H2C2_5: C2H2-type 96.8 0.00091 2E-08 29.9 1.6 23 76-99 1-23 (24)
41 COG5048 FOG: Zn-finger [Genera 96.8 0.00094 2E-08 50.8 2.5 56 2-59 293-354 (467)
42 PF12874 zf-met: Zinc-finger o 96.7 0.00086 1.9E-08 30.2 1.1 23 29-51 1-23 (25)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.00081 1.8E-08 31.0 0.5 22 76-97 2-23 (27)
44 KOG1146 Homeobox protein [Gene 96.4 0.0032 6.8E-08 53.9 3.1 93 2-97 440-540 (1406)
45 PF13913 zf-C2HC_2: zinc-finge 95.9 0.006 1.3E-07 27.6 1.6 21 76-97 3-23 (25)
46 PF13909 zf-H2C2_5: C2H2-type 95.8 0.0068 1.5E-07 26.9 1.5 23 29-52 1-23 (24)
47 PF12171 zf-C2H2_jaz: Zinc-fin 95.6 0.0036 7.8E-08 28.8 0.2 22 29-50 2-23 (27)
48 PF12756 zf-C2H2_2: C2H2 type 95.4 0.013 2.8E-07 35.5 2.3 24 28-51 50-73 (100)
49 KOG2893 Zn finger protein [Gen 95.1 0.0078 1.7E-07 42.4 0.5 48 29-99 11-59 (341)
50 PRK04860 hypothetical protein; 95.0 0.019 4.2E-07 38.4 2.2 38 74-115 118-156 (160)
51 smart00451 ZnF_U1 U1-like zinc 94.9 0.021 4.6E-07 27.7 1.7 23 75-97 3-25 (35)
52 COG5189 SFP1 Putative transcri 94.7 0.031 6.7E-07 41.1 2.9 26 72-97 346-373 (423)
53 smart00451 ZnF_U1 U1-like zinc 94.6 0.031 6.7E-07 27.1 1.9 23 28-50 3-25 (35)
54 PF05605 zf-Di19: Drought indu 93.1 0.11 2.3E-06 28.1 2.5 35 75-110 2-39 (54)
55 COG5048 FOG: Zn-finger [Genera 93.0 0.055 1.2E-06 41.1 1.6 61 28-105 289-353 (467)
56 COG4049 Uncharacterized protei 90.8 0.13 2.8E-06 27.8 1.0 28 70-97 12-39 (65)
57 KOG2186 Cell growth-regulating 88.5 0.39 8.5E-06 34.4 2.3 47 28-96 3-49 (276)
58 cd00350 rubredoxin_like Rubred 86.8 0.47 1E-05 22.8 1.4 10 74-83 16-25 (33)
59 smart00614 ZnF_BED BED zinc fi 86.8 0.61 1.3E-05 24.7 1.9 24 76-99 19-48 (50)
60 PF09986 DUF2225: Uncharacteri 86.7 0.22 4.7E-06 35.1 0.2 20 26-45 3-22 (214)
61 PF05443 ROS_MUCR: ROS/MUCR tr 85.7 0.48 1E-05 30.7 1.4 30 73-105 70-99 (132)
62 KOG4167 Predicted DNA-binding 85.4 0.22 4.7E-06 40.8 -0.4 28 74-101 791-818 (907)
63 KOG1146 Homeobox protein [Gene 84.1 0.53 1.2E-05 41.1 1.3 70 26-98 1282-1351(1406)
64 COG4049 Uncharacterized protei 83.7 0.59 1.3E-05 25.3 0.9 32 21-52 10-41 (65)
65 PF02892 zf-BED: BED zinc fing 83.6 1.1 2.4E-05 22.9 2.0 24 73-96 14-41 (45)
66 smart00734 ZnF_Rad18 Rad18-lik 83.1 0.94 2E-05 20.5 1.4 20 76-96 2-21 (26)
67 PF09538 FYDLN_acid: Protein o 81.1 0.9 2E-05 28.4 1.2 15 74-88 25-39 (108)
68 cd00729 rubredoxin_SM Rubredox 78.6 1.5 3.2E-05 21.2 1.3 10 74-83 17-26 (34)
69 COG2888 Predicted Zn-ribbon RN 77.7 2.3 4.9E-05 23.4 1.9 11 73-83 48-58 (61)
70 PRK00398 rpoP DNA-directed RNA 76.3 1.5 3.2E-05 22.7 1.0 12 75-86 21-32 (46)
71 TIGR02098 MJ0042_CXXC MJ0042 f 76.2 1.1 2.4E-05 22.0 0.5 14 29-42 3-16 (38)
72 TIGR00622 ssl1 transcription f 74.9 9.2 0.0002 24.0 4.3 74 26-99 13-105 (112)
73 COG1997 RPL43A Ribosomal prote 74.4 2.8 6.2E-05 25.0 1.9 31 56-88 35-66 (89)
74 KOG2893 Zn finger protein [Gen 74.0 0.76 1.7E-05 32.7 -0.7 42 11-52 17-59 (341)
75 PF13719 zinc_ribbon_5: zinc-r 73.1 3 6.6E-05 20.5 1.6 14 73-86 23-36 (37)
76 smart00531 TFIIE Transcription 72.6 2.6 5.7E-05 27.7 1.7 18 25-42 96-113 (147)
77 COG4957 Predicted transcriptio 70.7 2.3 5E-05 27.5 1.0 27 75-104 76-102 (148)
78 TIGR00373 conserved hypothetic 70.7 3.1 6.6E-05 27.8 1.7 21 24-44 105-125 (158)
79 KOG4124 Putative transcription 69.9 1.4 3E-05 33.2 -0.1 69 26-95 347-418 (442)
80 PRK14890 putative Zn-ribbon RN 69.8 4 8.7E-05 22.5 1.7 11 73-83 46-56 (59)
81 PRK06266 transcription initiat 68.9 3.2 6.9E-05 28.4 1.5 20 25-44 114-133 (178)
82 PF12013 DUF3505: Protein of u 68.4 4.1 8.9E-05 25.2 1.8 70 27-100 10-109 (109)
83 TIGR02300 FYDLN_acid conserved 68.0 3.4 7.4E-05 26.5 1.4 20 73-92 24-43 (129)
84 smart00659 RPOLCX RNA polymera 67.5 3.9 8.5E-05 21.1 1.3 13 28-40 2-14 (44)
85 PF04959 ARS2: Arsenite-resist 67.0 4.3 9.3E-05 28.6 1.8 29 24-52 73-101 (214)
86 KOG4167 Predicted DNA-binding 65.9 1.2 2.6E-05 36.7 -1.2 26 28-53 792-817 (907)
87 PF01927 Mut7-C: Mut7-C RNAse 65.5 5 0.00011 26.4 1.8 22 73-94 122-143 (147)
88 PRK00464 nrdR transcriptional 65.1 4.8 0.0001 26.9 1.7 18 74-91 27-44 (154)
89 KOG2186 Cell growth-regulating 63.9 4.3 9.2E-05 29.3 1.3 40 75-115 3-42 (276)
90 PHA00626 hypothetical protein 63.7 6.9 0.00015 21.3 1.8 15 74-88 22-36 (59)
91 PF07754 DUF1610: Domain of un 63.5 3.3 7.2E-05 18.4 0.5 10 74-83 15-24 (24)
92 PF04810 zf-Sec23_Sec24: Sec23 62.4 6 0.00013 19.8 1.4 18 67-84 16-33 (40)
93 smart00834 CxxC_CXXC_SSSS Puta 62.3 3.6 7.8E-05 20.3 0.6 30 75-110 5-34 (41)
94 KOG2231 Predicted E3 ubiquitin 62.3 9.3 0.0002 31.6 3.1 25 77-101 184-208 (669)
95 PF05290 Baculo_IE-1: Baculovi 61.0 3.7 8E-05 26.6 0.6 20 22-41 74-93 (140)
96 PF09723 Zn-ribbon_8: Zinc rib 59.9 4.2 9E-05 20.6 0.6 30 75-110 5-34 (42)
97 COG1592 Rubrerythrin [Energy p 59.6 5.4 0.00012 26.9 1.2 23 56-82 134-156 (166)
98 PRK09678 DNA-binding transcrip 59.4 6 0.00013 22.8 1.2 19 73-91 25-45 (72)
99 PF06524 NOA36: NOA36 protein; 59.3 5.7 0.00012 28.8 1.3 76 23-99 137-233 (314)
100 KOG2785 C2H2-type Zn-finger pr 58.5 5.4 0.00012 30.5 1.1 70 28-97 3-90 (390)
101 PF10571 UPF0547: Uncharacteri 58.4 4.5 9.8E-05 18.3 0.5 11 76-86 15-25 (26)
102 KOG2785 C2H2-type Zn-finger pr 56.7 14 0.00031 28.3 3.1 68 27-97 165-242 (390)
103 PTZ00255 60S ribosomal protein 56.5 4.7 0.0001 24.3 0.5 15 74-88 53-67 (90)
104 PF04959 ARS2: Arsenite-resist 56.1 4.4 9.6E-05 28.6 0.4 25 73-97 75-99 (214)
105 PF15269 zf-C2H2_7: Zinc-finge 56.1 8.3 0.00018 19.9 1.3 22 76-97 21-42 (54)
106 KOG4173 Alpha-SNAP protein [In 55.5 3.6 7.8E-05 28.7 -0.2 84 2-100 85-172 (253)
107 cd00924 Cyt_c_Oxidase_Vb Cytoc 53.7 6.7 0.00015 24.0 0.8 19 21-40 73-91 (97)
108 smart00154 ZnF_AN1 AN1-like Zi 52.6 7 0.00015 19.5 0.7 14 75-88 12-25 (39)
109 PF01780 Ribosomal_L37ae: Ribo 52.0 3.9 8.5E-05 24.6 -0.4 13 75-87 53-65 (90)
110 PF12013 DUF3505: Protein of u 51.2 14 0.00031 22.8 2.1 25 29-53 81-109 (109)
111 PLN02294 cytochrome c oxidase 50.9 8.2 0.00018 26.1 1.0 20 68-88 135-154 (174)
112 COG4530 Uncharacterized protei 50.3 7.5 0.00016 24.3 0.7 15 73-87 24-38 (129)
113 TIGR02605 CxxC_CxxC_SSSS putat 50.1 7.4 0.00016 20.4 0.6 30 75-110 5-34 (52)
114 COG5236 Uncharacterized conser 49.4 47 0.001 25.4 4.7 69 30-99 222-305 (493)
115 KOG3408 U1-like Zn-finger-cont 49.4 11 0.00024 24.0 1.3 25 73-97 55-79 (129)
116 TIGR00280 L37a ribosomal prote 48.7 6.4 0.00014 23.7 0.2 14 75-88 53-66 (91)
117 COG3357 Predicted transcriptio 48.6 9.2 0.0002 23.0 0.8 14 27-40 57-70 (97)
118 KOG0717 Molecular chaperone (D 48.4 11 0.00024 29.7 1.4 21 76-96 293-313 (508)
119 PF01428 zf-AN1: AN1-like Zinc 47.8 7.2 0.00016 19.8 0.3 15 74-88 12-26 (43)
120 PF09845 DUF2072: Zn-ribbon co 47.6 8.5 0.00018 24.9 0.6 15 75-89 1-15 (131)
121 PF13451 zf-trcl: Probable zin 47.5 9.4 0.0002 20.2 0.7 18 73-90 2-19 (49)
122 PF13717 zinc_ribbon_4: zinc-r 46.7 13 0.00029 18.1 1.1 11 28-38 25-35 (36)
123 PF10276 zf-CHCC: Zinc-finger 46.3 10 0.00023 19.1 0.7 12 27-38 28-39 (40)
124 PF04423 Rad50_zn_hook: Rad50 45.4 8.2 0.00018 20.6 0.3 12 77-88 22-33 (54)
125 COG3677 Transposase and inacti 44.5 16 0.00034 23.6 1.5 16 73-88 51-66 (129)
126 PF13878 zf-C2H2_3: zinc-finge 44.3 2.9 6.3E-05 21.1 -1.5 21 3-23 18-38 (41)
127 COG1198 PriA Primosomal protei 42.3 8.9 0.00019 32.2 0.2 48 30-84 437-484 (730)
128 PRK03976 rpl37ae 50S ribosomal 42.2 8.7 0.00019 23.1 0.1 14 75-88 54-67 (90)
129 KOG2071 mRNA cleavage and poly 41.9 18 0.00039 29.4 1.8 28 25-52 415-442 (579)
130 PRK12380 hydrogenase nickel in 41.2 15 0.00032 23.1 1.0 15 26-40 68-82 (113)
131 PF08790 zf-LYAR: LYAR-type C2 40.8 9 0.0002 17.7 -0.0 19 76-95 1-19 (28)
132 PF01096 TFIIS_C: Transcriptio 39.8 24 0.00052 17.5 1.5 11 75-85 28-38 (39)
133 KOG3408 U1-like Zn-finger-cont 39.6 20 0.00043 22.9 1.4 24 27-50 56-79 (129)
134 KOG2071 mRNA cleavage and poly 39.4 19 0.00042 29.2 1.6 29 73-101 416-444 (579)
135 PF01363 FYVE: FYVE zinc finge 38.9 16 0.00035 20.3 0.8 12 28-39 9-20 (69)
136 TIGR00100 hypA hydrogenase nic 38.8 18 0.00038 22.8 1.1 19 22-40 64-82 (115)
137 PRK14873 primosome assembly pr 38.4 26 0.00057 29.2 2.2 47 30-84 385-431 (665)
138 KOG2807 RNA polymerase II tran 38.2 70 0.0015 24.3 4.1 69 27-99 289-369 (378)
139 KOG2482 Predicted C2H2-type Zn 38.0 30 0.00064 26.4 2.2 29 75-103 195-225 (423)
140 PF04780 DUF629: Protein of un 37.8 23 0.0005 28.1 1.8 28 75-102 57-85 (466)
141 PF07282 OrfB_Zn_ribbon: Putat 37.7 27 0.00059 19.4 1.7 15 73-87 44-58 (69)
142 PRK00564 hypA hydrogenase nick 36.7 21 0.00045 22.6 1.2 19 22-40 65-83 (117)
143 COG3364 Zn-ribbon containing p 35.9 20 0.00042 22.2 0.9 16 75-90 2-17 (112)
144 PF10013 DUF2256: Uncharacteri 35.6 16 0.00034 18.7 0.4 15 76-90 9-23 (42)
145 KOG2636 Splicing factor 3a, su 35.4 26 0.00056 27.6 1.7 29 68-96 394-423 (497)
146 PF15135 UPF0515: Uncharacteri 35.4 45 0.00097 24.2 2.7 59 22-88 106-168 (278)
147 COG1773 Rubredoxin [Energy pro 35.2 18 0.00038 19.7 0.6 15 74-88 2-16 (55)
148 PF12760 Zn_Tnp_IS1595: Transp 34.2 41 0.00089 17.2 1.9 11 73-83 35-45 (46)
149 KOG1842 FYVE finger-containing 33.5 22 0.00048 28.0 1.0 28 74-101 14-42 (505)
150 PRK03681 hypA hydrogenase nick 33.5 24 0.00051 22.2 1.0 16 24-39 66-81 (114)
151 cd00065 FYVE FYVE domain; Zinc 33.2 29 0.00062 18.3 1.2 11 30-40 4-14 (57)
152 KOG2593 Transcription initiati 33.1 30 0.00065 27.1 1.7 21 23-43 123-143 (436)
153 PF01215 COX5B: Cytochrome c o 32.9 20 0.00043 23.4 0.6 20 68-88 106-125 (136)
154 TIGR00595 priA primosomal prot 32.7 13 0.00029 29.7 -0.2 47 30-83 215-261 (505)
155 smart00440 ZnF_C2C2 C2C2 Zinc 32.4 50 0.0011 16.4 1.9 12 75-86 28-39 (40)
156 PHA02998 RNA polymerase subuni 31.4 39 0.00085 23.2 1.8 12 76-87 172-183 (195)
157 PF08271 TF_Zn_Ribbon: TFIIB z 31.0 32 0.0007 17.2 1.1 11 75-85 19-29 (43)
158 PTZ00448 hypothetical protein; 31.0 32 0.00068 26.4 1.5 25 75-99 314-338 (373)
159 KOG2482 Predicted C2H2-type Zn 30.8 32 0.0007 26.2 1.5 23 28-50 195-217 (423)
160 PF11931 DUF3449: Domain of un 30.1 17 0.00037 25.3 0.0 29 68-96 94-123 (196)
161 TIGR01206 lysW lysine biosynth 30.1 22 0.00047 19.2 0.4 31 75-112 2-32 (54)
162 PF14353 CpXC: CpXC protein 29.2 25 0.00053 22.4 0.6 22 74-95 37-58 (128)
163 PTZ00043 cytochrome c oxidase 29.0 27 0.00059 24.9 0.8 15 73-87 179-193 (268)
164 PF07295 DUF1451: Protein of u 28.9 28 0.00062 23.0 0.9 6 77-82 132-137 (146)
165 COG1571 Predicted DNA-binding 28.7 32 0.00069 26.9 1.2 16 74-89 366-381 (421)
166 TIGR00416 sms DNA repair prote 26.7 45 0.00098 26.4 1.8 11 74-84 20-30 (454)
167 PF08209 Sgf11: Sgf11 (transcr 26.5 74 0.0016 15.2 1.9 24 75-99 4-27 (33)
168 PF11238 DUF3039: Protein of u 26.1 31 0.00068 18.9 0.6 26 2-38 29-54 (58)
169 PF07975 C1_4: TFIIH C1-like d 26.0 18 0.00039 19.3 -0.4 26 74-99 20-45 (51)
170 PRK11823 DNA repair protein Ra 26.0 48 0.001 26.2 1.8 12 27-38 6-17 (446)
171 smart00064 FYVE Protein presen 25.7 45 0.00097 18.4 1.2 11 29-39 11-21 (68)
172 PF03604 DNA_RNApol_7kD: DNA d 25.7 32 0.0007 16.3 0.5 11 76-86 1-11 (32)
173 PF06397 Desulfoferrod_N: Desu 25.3 33 0.00072 16.8 0.5 12 27-38 5-16 (36)
174 KOG1813 Predicted E3 ubiquitin 25.1 44 0.00095 24.9 1.3 59 26-97 239-301 (313)
175 PF09416 UPF1_Zn_bind: RNA hel 25.1 30 0.00064 23.1 0.4 20 3-22 19-38 (152)
176 COG1996 RPC10 DNA-directed RNA 24.8 31 0.00066 18.3 0.4 13 73-85 4-16 (49)
177 KOG0717 Molecular chaperone (D 24.8 48 0.001 26.4 1.5 21 29-49 293-313 (508)
178 COG5188 PRP9 Splicing factor 3 24.6 46 0.001 25.5 1.4 29 68-96 367-396 (470)
179 PF01286 XPA_N: XPA protein N- 24.5 32 0.00069 16.7 0.4 13 77-89 5-17 (34)
180 COG0068 HypF Hydrogenase matur 23.9 19 0.0004 30.1 -0.8 51 30-83 125-181 (750)
181 KOG2231 Predicted E3 ubiquitin 23.6 74 0.0016 26.6 2.4 72 30-105 184-273 (669)
182 smart00661 RPOL9 RNA polymeras 23.4 86 0.0019 16.1 2.0 12 75-86 20-31 (52)
183 PF05191 ADK_lid: Adenylate ki 22.9 36 0.00079 16.6 0.4 12 76-87 2-13 (36)
184 COG5112 UFD2 U1-like Zn-finger 22.3 43 0.00093 20.8 0.7 24 73-96 53-76 (126)
185 TIGR00686 phnA alkylphosphonat 22.2 48 0.001 20.7 0.9 15 74-88 18-32 (109)
186 PRK03824 hypA hydrogenase nick 21.9 56 0.0012 21.2 1.3 20 22-41 64-83 (135)
187 PF00301 Rubredoxin: Rubredoxi 21.8 43 0.00092 17.5 0.6 13 76-88 2-14 (47)
188 PF14787 zf-CCHC_5: GAG-polypr 21.7 38 0.00083 16.6 0.3 14 77-90 4-17 (36)
189 PF08792 A2L_zn_ribbon: A2L zi 21.4 47 0.001 15.8 0.6 12 75-86 21-32 (33)
190 cd00730 rubredoxin Rubredoxin; 21.3 38 0.00083 17.9 0.3 13 76-88 2-14 (50)
191 COG3091 SprT Zn-dependent meta 21.3 43 0.00094 22.3 0.6 10 75-84 140-149 (156)
192 PF06044 DRP: Dam-replacing fa 21.1 42 0.0009 24.3 0.6 31 58-88 33-66 (254)
193 KOG0978 E3 ubiquitin ligase in 20.9 31 0.00066 28.9 -0.2 22 73-94 676-697 (698)
194 PLN02748 tRNA dimethylallyltra 20.8 62 0.0014 25.8 1.5 24 74-97 417-441 (468)
195 PF14369 zf-RING_3: zinc-finge 20.7 65 0.0014 15.5 1.0 10 30-39 23-32 (35)
196 cd01121 Sms Sms (bacterial rad 20.7 65 0.0014 24.8 1.6 11 74-84 13-23 (372)
197 PF02748 PyrI_C: Aspartate car 20.7 47 0.001 17.7 0.6 18 71-88 31-48 (52)
198 PRK03564 formate dehydrogenase 20.4 51 0.0011 24.8 0.9 50 25-83 184-234 (309)
199 PRK08222 hydrogenase 4 subunit 20.3 62 0.0014 22.1 1.3 21 74-94 113-133 (181)
200 COG1656 Uncharacterized conser 20.2 68 0.0015 21.7 1.4 23 74-96 129-151 (165)
201 PTZ00303 phosphatidylinositol 20.2 83 0.0018 27.1 2.1 13 76-88 461-473 (1374)
202 PRK04023 DNA polymerase II lar 20.1 84 0.0018 27.8 2.2 10 28-37 626-635 (1121)
No 1
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.92 E-value=7.5e-26 Score=157.83 Aligned_cols=124 Identities=23% Similarity=0.294 Sum_probs=111.4
Q ss_pred cchhcccCCCCCCCccccccccC---CCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc---------ccccc
Q 041414 2 ANCLMFMPHGGDFDAVNGVNMAV---ADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV---------DTQQS 69 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~~h~---~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~---------~h~~~ 69 (152)
..||+++++.+.|. +|.++|- ..+.+.|++|+|.|.+-..|+.|+++|+ -+++|..|++ .|+++
T Consensus 134 ~eCgk~ysT~snLs--rHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPWLLQGHiRT 209 (279)
T KOG2462|consen 134 PECGKSYSTSSNLS--RHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPWLLQGHIRT 209 (279)
T ss_pred cccccccccccccc--hhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccccchHHhhccccc
Confidence 46999999999999 9999993 3678999999999999999999999998 4788988886 89999
Q ss_pred cCCCCceeccccccccccchHHHHHHhhccCCCccc-ccccccccCCCCCcchhhhccCcc
Q 041414 70 PVKPKTHECSVCGLEFAIGQALGGHMRRHRAGASHA-NEKLSAFSSLSDTAPLVEKANSRR 129 (152)
Q Consensus 70 h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 129 (152)
|+|||||.|+.|+|+|...++|+.||++|.+.|.|. ..|+++|+...-+..+..+.-...
T Consensus 210 HTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~C~~~ 270 (279)
T KOG2462|consen 210 HTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESACLKY 270 (279)
T ss_pred ccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhccccc
Confidence 999999999999999999999999999999999998 899999999887777766654433
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.84 E-value=3.1e-22 Score=139.83 Aligned_cols=92 Identities=22% Similarity=0.340 Sum_probs=84.0
Q ss_pred cchhcccCCCCCCCccccccccCCCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc---------ccccccCC
Q 041414 2 ANCLMFMPHGGDFDAVNGVNMAVADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV---------DTQQSPVK 72 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~~h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~---------~h~~~h~~ 72 (152)
..|+|.+.+-..|. .|+++|+ -+++|.+|||.|....-|+.|+|+|+|+|||.|..|++ .|+++|++
T Consensus 165 ~~C~K~YvSmpALk--MHirTH~--l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~ 240 (279)
T KOG2462|consen 165 KYCGKVYVSMPALK--MHIRTHT--LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSD 240 (279)
T ss_pred CCCCceeeehHHHh--hHhhccC--CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcC
Confidence 36889987777777 9999987 78999999999999999999999999999999999986 79999999
Q ss_pred CCceeccccccccccchHHHHHHhh
Q 041414 73 PKTHECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
.|.|+|..|+|+|...+.|.+|...
T Consensus 241 ~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 241 VKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred CccccCcchhhHHHHHHHHHHhhhh
Confidence 9999999999999999999999864
No 3
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.69 E-value=4.1e-18 Score=133.74 Aligned_cols=48 Identities=19% Similarity=0.434 Sum_probs=44.5
Q ss_pred chhcccCCCCCCCccccccccCCCcceecCcccccCCChhHHHHHHHhcC
Q 041414 3 NCLMFMPHGGDFDAVNGVNMAVADRAFECKTCNRQFPSFQALGGHRASHK 52 (152)
Q Consensus 3 ~C~~~~~~~~~~~~~~h~~~h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~ 52 (152)
.|.|.|.+.+.|. +|.+.||||+||.|++||..|..+.+|+.|...|.
T Consensus 358 ~CakvfgS~SaLq--iHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~ 405 (958)
T KOG1074|consen 358 FCAKVFGSDSALQ--IHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHR 405 (958)
T ss_pred hhHhhcCchhhhh--hhhhccCCCCCeeecccccccccccceeeeeeecc
Confidence 5999999999988 99999999999999999999999999999976654
No 4
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.48 E-value=1.5e-15 Score=102.31 Aligned_cols=74 Identities=19% Similarity=0.415 Sum_probs=58.8
Q ss_pred CCCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc---------ccccccCCCCceeccccccccccchHHHHH
Q 041414 24 VADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV---------DTQQSPVKPKTHECSVCGLEFAIGQALGGH 94 (152)
Q Consensus 24 ~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~---------~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H 94 (152)
.+...|.|.+|+|.|.....|.+|++-|...+.+-|..|++ +|.++|+|.+||+|..|+|+|.+...|..|
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 45566888888888888888888888887777776766665 777888888899999999999999889888
Q ss_pred Hhh
Q 041414 95 MRR 97 (152)
Q Consensus 95 ~~~ 97 (152)
++.
T Consensus 193 l~k 195 (267)
T KOG3576|consen 193 LKK 195 (267)
T ss_pred HHH
Confidence 763
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.45 E-value=1.1e-14 Score=113.53 Aligned_cols=73 Identities=19% Similarity=0.383 Sum_probs=68.4
Q ss_pred CCCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc---------ccccccCCCCceeccccccccccchHHHHH
Q 041414 24 VADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV---------DTQQSPVKPKTHECSVCGLEFAIGQALGGH 94 (152)
Q Consensus 24 ~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~---------~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H 94 (152)
+.+..|.|+.|+|.|...++|.+|.--|+|.+||+|..|.+ .|+|.|+|||||.|..|+|.|...+...+|
T Consensus 890 te~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQH 969 (1007)
T KOG3623|consen 890 TEDGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQH 969 (1007)
T ss_pred CccccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhh
Confidence 56779999999999999999999999999999999999986 678999999999999999999999999999
Q ss_pred Hh
Q 041414 95 MR 96 (152)
Q Consensus 95 ~~ 96 (152)
|.
T Consensus 970 MN 971 (1007)
T KOG3623|consen 970 MN 971 (1007)
T ss_pred hc
Confidence 96
No 6
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.43 E-value=1.6e-14 Score=113.82 Aligned_cols=82 Identities=24% Similarity=0.474 Sum_probs=75.1
Q ss_pred cchhcccCCCCCCCccccccccCCCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceecc--
Q 041414 2 ANCLMFMPHGGDFDAVNGVNMAVADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECS-- 79 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~~h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~-- 79 (152)
..|.+.+++++.|+ .|.++|+||+||+|.+||++|..+.+|+.|+-+|...-++ .-+|.|+
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 9999999999999999999999999999999999776554 3579999
Q ss_pred -ccccccccchHHHHHHhhccC
Q 041414 80 -VCGLEFAIGQALGGHMRRHRA 100 (152)
Q Consensus 80 -~C~k~F~~~~~L~~H~~~h~~ 100 (152)
+|-+.|...-.|.+|+++|.+
T Consensus 672 ~ic~~kftn~V~lpQhIriH~~ 693 (958)
T KOG1074|consen 672 FICQKKFTNAVTLPQHIRIHLG 693 (958)
T ss_pred hhhcccccccccccceEEeecC
Confidence 999999999999999999984
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.37 E-value=1.2e-13 Score=107.77 Aligned_cols=70 Identities=14% Similarity=0.202 Sum_probs=62.6
Q ss_pred CCCCCCCCCCc---------ccccccCCCCceeccccccccccchHHHHHHhhccCCCccc-ccccccccCCCCCcchhh
Q 041414 54 SRVTEGSGGGV---------DTQQSPVKPKTHECSVCGLEFAIGQALGGHMRRHRAGASHA-NEKLSAFSSLSDTAPLVE 123 (152)
Q Consensus 54 ~~~~~c~~~~~---------~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~-~~~~~~~~~~~~~~~~~~ 123 (152)
.-+|.|+.|.+ +|..-|+|.+||+|.+|.|+|..+.+|..|+|.|.|+|||. ..|++.|+-+.+-+.++.
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 34688988875 88899999999999999999999999999999999999997 899999999877776654
No 8
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.35 E-value=2.7e-14 Score=103.34 Aligned_cols=135 Identities=13% Similarity=0.165 Sum_probs=95.4
Q ss_pred cchhcccCCCCCCCccccccccCCCcceecCcccccCCChhHHHHHHHhcC--CCCCCCCCCC-----------------
Q 041414 2 ANCLMFMPHGGDFDAVNGVNMAVADRAFECKTCNRQFPSFQALGGHRASHK--KSRVTEGSGG----------------- 62 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~~h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~--~~~~~~c~~~----------------- 62 (152)
|.|.+.|.++..|. .|++.|++||...|+.||.-|..+..|-.|.+..+ ...+|.|..|
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 57888888888888 99999999999999999999998888888865432 3334444333
Q ss_pred ---------Cc---------cccc-ccCCCCceeccccccccccchHHHHHHhhccCCCccc---ccccccccCCCCCcc
Q 041414 63 ---------GV---------DTQQ-SPVKPKTHECSVCGLEFAIGQALGGHMRRHRAGASHA---NEKLSAFSSLSDTAP 120 (152)
Q Consensus 63 ---------~~---------~h~~-~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~---~~~~~~~~~~~~~~~ 120 (152)
.. .|++ .|+..|||+|..|++.|.+.+.|.+|..+|. +..|. +.|..++........
T Consensus 261 vn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~~q~~~ 339 (467)
T KOG3608|consen 261 VNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTYTQMRR 339 (467)
T ss_pred hhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHHHHHHH
Confidence 21 5554 5778899999999999999999999999888 55554 457666666555555
Q ss_pred hhhhccCcceeecccCCCCCCCchh
Q 041414 121 LVEKANSRRVLCLDLNLTPYENDLE 145 (152)
Q Consensus 121 ~~~~~~~~~~~~~~~~~~p~~~d~~ 145 (152)
+.+..+ ...|.++|-+-++
T Consensus 340 H~~evh------Eg~np~~Y~CH~C 358 (467)
T KOG3608|consen 340 HFLEVH------EGNNPILYACHCC 358 (467)
T ss_pred HHHHhc------cCCCCCceeeecc
Confidence 544332 1233456666443
No 9
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.34 E-value=1.2e-13 Score=93.21 Aligned_cols=75 Identities=19% Similarity=0.192 Sum_probs=64.9
Q ss_pred CCCCCCCCCCCCc---------ccccccCCCCceeccccccccccchHHHHHHhhccCCCccc-ccccccccCCCCCcch
Q 041414 52 KKSRVTEGSGGGV---------DTQQSPVKPKTHECSVCGLEFAIGQALGGHMRRHRAGASHA-NEKLSAFSSLSDTAPL 121 (152)
Q Consensus 52 ~~~~~~~c~~~~~---------~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~-~~~~~~~~~~~~~~~~ 121 (152)
.+...+.|..|++ +|++.|...|.|-|..|||.|...-.|++|+++|+|.+||. ..|+++|.+.-++..+
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcslesh 192 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESH 192 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHH
Confidence 3445577888876 89999999999999999999999999999999999999998 8999999998877777
Q ss_pred hhhcc
Q 041414 122 VEKAN 126 (152)
Q Consensus 122 ~~~~~ 126 (152)
.++.+
T Consensus 193 l~kvh 197 (267)
T KOG3576|consen 193 LKKVH 197 (267)
T ss_pred HHHHc
Confidence 66644
No 10
>PHA00733 hypothetical protein
Probab=99.21 E-value=1.6e-11 Score=78.92 Aligned_cols=76 Identities=20% Similarity=0.280 Sum_probs=50.2
Q ss_pred chhcccCCCCCCCcc----ccccccCCCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceec
Q 041414 3 NCLMFMPHGGDFDAV----NGVNMAVADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHEC 78 (152)
Q Consensus 3 ~C~~~~~~~~~~~~~----~h~~~h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C 78 (152)
.|.+.|.....|... .|+.. .+++||.|+.|++.|.....|..|++.+ +.+|.|
T Consensus 45 ~~~~~~~~~~~l~~~~~l~~~~~~-~~~kPy~C~~Cgk~Fss~s~L~~H~r~h---------------------~~~~~C 102 (128)
T PHA00733 45 VVKTLIYNPQLLDESSYLYKLLTS-KAVSPYVCPLCLMPFSSSVSLKQHIRYT---------------------EHSKVC 102 (128)
T ss_pred HHhhhccChhhhcchHHHHhhccc-CCCCCccCCCCCCcCCCHHHHHHHHhcC---------------------CcCccC
Confidence 355555555555422 33333 3467777888888887777777777654 235788
Q ss_pred cccccccccchHHHHHHhhccC
Q 041414 79 SVCGLEFAIGQALGGHMRRHRA 100 (152)
Q Consensus 79 ~~C~k~F~~~~~L~~H~~~h~~ 100 (152)
..|+++|.....|..|+...++
T Consensus 103 ~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 103 PVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCCCccCCHHHHHHHHHHhcC
Confidence 8888888888888888776543
No 11
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.13 E-value=2.2e-11 Score=88.45 Aligned_cols=93 Identities=17% Similarity=0.301 Sum_probs=73.0
Q ss_pred cchhcccCCCCCCCccccccc-cCCCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCC--CCc---------cccc-
Q 041414 2 ANCLMFMPHGGDFDAVNGVNM-AVADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSG--GGV---------DTQQ- 68 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~~-h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~--~~~---------~h~~- 68 (152)
++|.|..+..++|. .||+. |+..+||+|+.|++.|...+.|.+|..+|+ +-.|.|+. |.. +|.+
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 57888888888888 88875 778899999999999999999999988887 55677765 442 4443
Q ss_pred ccCCC--CceeccccccccccchHHHHHHhh
Q 041414 69 SPVKP--KTHECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 69 ~h~~~--k~~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
.|.|. .+|.|..|++.|.+..+|.+|+..
T Consensus 344 vhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~k 374 (467)
T KOG3608|consen 344 VHEGNNPILYACHCCDRFFTSGKSLSAHLMK 374 (467)
T ss_pred hccCCCCCceeeecchhhhccchhHHHHHHH
Confidence 45443 469999999999999999999754
No 12
>PHA02768 hypothetical protein; Provisional
Probab=99.07 E-value=6.4e-11 Score=63.98 Aligned_cols=44 Identities=16% Similarity=0.230 Sum_probs=38.6
Q ss_pred ceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccccccchHHH
Q 041414 28 AFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALG 92 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~ 92 (152)
-|.|++||+.|...++|..|+++|+ ++|+|..|++.|...+.|.
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 4799999999999999999999985 3789999999999877653
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.89 E-value=3.6e-09 Score=82.54 Aligned_cols=83 Identities=14% Similarity=0.222 Sum_probs=66.4
Q ss_pred ceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc--------ccccccCCCCceecccccccccc----------ch
Q 041414 28 AFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV--------DTQQSPVKPKTHECSVCGLEFAI----------GQ 89 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~--------~h~~~h~~~k~~~C~~C~k~F~~----------~~ 89 (152)
.+.|+.|++.|. ...|..|+.+++ +++.|. |+. .|+..|.+++++.|..|++.|.. ..
T Consensus 453 H~~C~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s 528 (567)
T PLN03086 453 HVHCEKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLR 528 (567)
T ss_pred CccCCCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhh
Confidence 358999999996 678999999985 678887 754 78888999999999999999952 35
Q ss_pred HHHHHHhhccCCCccc-ccccccccCC
Q 041414 90 ALGGHMRRHRAGASHA-NEKLSAFSSL 115 (152)
Q Consensus 90 ~L~~H~~~h~~~~~~~-~~~~~~~~~~ 115 (152)
.|..|..++ |.+++. ..|++.+...
T Consensus 529 ~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr 554 (567)
T PLN03086 529 GMSEHESIC-GSRTAPCDSCGRSVMLK 554 (567)
T ss_pred hHHHHHHhc-CCcceEccccCCeeeeh
Confidence 899999987 555554 7888776653
No 14
>PHA02768 hypothetical protein; Provisional
Probab=98.79 E-value=3.9e-09 Score=57.07 Aligned_cols=42 Identities=17% Similarity=0.329 Sum_probs=35.5
Q ss_pred ceeccccccccccchHHHHHHhhccCCCccc-ccccccccCCCCC
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRAGASHA-NEKLSAFSSLSDT 118 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~-~~~~~~~~~~~~~ 118 (152)
.|+|+.||+.|...++|..|+++|+ +++. ..|++.|+.....
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceeccccee
Confidence 5899999999999999999999999 4554 8899988865443
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=98.78 E-value=7.4e-10 Score=51.38 Aligned_cols=23 Identities=13% Similarity=0.596 Sum_probs=21.4
Q ss_pred cccccccCCCcceecCcccccCC
Q 041414 17 VNGVNMAVADRAFECKTCNRQFP 39 (152)
Q Consensus 17 ~~h~~~h~~e~~~~C~~C~k~f~ 39 (152)
..||++|++++||.|++|++.|.
T Consensus 3 ~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 3 RRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHhhhcCCCCCCCCCCCcCeeC
Confidence 38999999999999999999986
No 16
>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=98.73 E-value=9.1e-09 Score=47.65 Aligned_cols=26 Identities=31% Similarity=0.590 Sum_probs=20.7
Q ss_pred HHHHHHHhcCCCCCCCCCCCCcccccccCCCCceecccccccccc
Q 041414 43 ALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAI 87 (152)
Q Consensus 43 ~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~ 87 (152)
+|.+|+++|++ ++||.|+.|++.|.+
T Consensus 1 ~l~~H~~~H~~-------------------~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTG-------------------EKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSS-------------------SSSEEESSSSEEESS
T ss_pred CHHHHhhhcCC-------------------CCCCCCCCCcCeeCc
Confidence 46677777765 889999999999964
No 17
>PHA00733 hypothetical protein
Probab=98.65 E-value=6e-09 Score=67.08 Aligned_cols=87 Identities=15% Similarity=0.105 Sum_probs=64.7
Q ss_pred CCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccccccchHHHHHHhhccCCCcc
Q 041414 25 ADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGHMRRHRAGASH 104 (152)
Q Consensus 25 ~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~ 104 (152)
..+++.|.+|.+.|.....|..+.-... ++. +.+++||.|..||+.|.....|..|+++|.. ...
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~-------------~~~-~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~-~~~ 101 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYK-------------LLT-SKAVSPYVCPLCLMPFSSSVSLKQHIRYTEH-SKV 101 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHh-------------hcc-cCCCCCccCCCCCCcCCCHHHHHHHHhcCCc-Ccc
Confidence 4678999999999988877776622110 111 2237899999999999999999999997732 234
Q ss_pred cccccccccCCCCCcchhhhcc
Q 041414 105 ANEKLSAFSSLSDTAPLVEKAN 126 (152)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~ 126 (152)
+..|++.|.....+..++...+
T Consensus 102 C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 102 CPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred CCCCCCccCCHHHHHHHHHHhc
Confidence 5899999999887777666544
No 18
>PHA00732 hypothetical protein
Probab=98.60 E-value=3.3e-08 Score=58.16 Aligned_cols=47 Identities=26% Similarity=0.537 Sum_probs=37.4
Q ss_pred ceecCcccccCCChhHHHHHHHh-cCCCCCCCCCCCCcccccccCCCCceeccccccccccchHHHHHHhhcc
Q 041414 28 AFECKTCNRQFPSFQALGGHRAS-HKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGHMRRHR 99 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~-h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~ 99 (152)
||.|..|++.|....+|..|++. |. ++.|+.||+.|. .|..|..+..
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 68899999999999999999874 43 247999999998 4777876543
No 19
>PHA00616 hypothetical protein
Probab=98.56 E-value=2.9e-08 Score=51.14 Aligned_cols=31 Identities=16% Similarity=0.223 Sum_probs=28.8
Q ss_pred ceeccccccccccchHHHHHHhhccCCCccc
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRAGASHA 105 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~ 105 (152)
||+|+.||+.|...+.|..|++.|+|+++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 6899999999999999999999999997754
No 20
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.48 E-value=9.4e-08 Score=74.77 Aligned_cols=86 Identities=16% Similarity=0.322 Sum_probs=67.3
Q ss_pred chhcccCCCCCCCccccccccCCCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc------------------
Q 041414 3 NCLMFMPHGGDFDAVNGVNMAVADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV------------------ 64 (152)
Q Consensus 3 ~C~~~~~~~~~~~~~~h~~~h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~------------------ 64 (152)
.|++.|. ...+. .|+.+|. +++.|+ ||+.+ ....|..|+.+|...+++.|..|..
T Consensus 458 ~Cgk~f~-~s~Le--kH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~d~~s~L 530 (567)
T PLN03086 458 KCGQAFQ-QGEME--KHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVRDRLRGM 530 (567)
T ss_pred CCCCccc-hHHHH--HHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCccccchhhhhhhH
Confidence 5777775 45565 8988874 899999 99765 5689999999999999999988865
Q ss_pred -ccccccCCCCceeccccccccccchHHHHHHhh
Q 041414 65 -DTQQSPVKPKTHECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 65 -~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
.|... .|.+++.|..||+.|.... |..|+..
T Consensus 531 t~HE~~-CG~rt~~C~~Cgk~Vrlrd-m~~H~~~ 562 (567)
T PLN03086 531 SEHESI-CGSRTAPCDSCGRSVMLKE-MDIHQIA 562 (567)
T ss_pred HHHHHh-cCCcceEccccCCeeeehh-HHHHHHH
Confidence 23333 4889999999999987654 6677654
No 21
>PHA00616 hypothetical protein
Probab=98.48 E-value=5.9e-08 Score=50.02 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=28.6
Q ss_pred ceecCcccccCCChhHHHHHHHhcCCCCCCCC
Q 041414 28 AFECKTCNRQFPSFQALGGHRASHKKSRVTEG 59 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c 59 (152)
||.|+.||+.|...+.|..|++.|++++++.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 68999999999999999999999999766544
No 22
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.44 E-value=7.6e-08 Score=71.76 Aligned_cols=75 Identities=21% Similarity=0.438 Sum_probs=52.1
Q ss_pred cceecCcccccCCChhHHHHHHHhcCCCCCCC--C-CCCC------c---cccc--ccCCCCceeccccccccccchHHH
Q 041414 27 RAFECKTCNRQFPSFQALGGHRASHKKSRVTE--G-SGGG------V---DTQQ--SPVKPKTHECSVCGLEFAIGQALG 92 (152)
Q Consensus 27 ~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~--c-~~~~------~---~h~~--~h~~~k~~~C~~C~k~F~~~~~L~ 92 (152)
.-|+|++|+|.|....+|..|+|+|.-..... . ..-. . .-.+ ....+-.|.|..|+|.|.+...|+
T Consensus 294 vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 294 VEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred eeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHHH
Confidence 35999999999999999999999995322111 0 0000 0 0000 012234899999999999999999
Q ss_pred HHHhhccCC
Q 041414 93 GHMRRHRAG 101 (152)
Q Consensus 93 ~H~~~h~~~ 101 (152)
.|+.+|...
T Consensus 374 KHqlthq~~ 382 (500)
T KOG3993|consen 374 KHQLTHQRA 382 (500)
T ss_pred HhHHhhhcc
Confidence 999887643
No 23
>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=98.33 E-value=3.1e-07 Score=41.11 Aligned_cols=23 Identities=43% Similarity=0.911 Sum_probs=21.6
Q ss_pred eeccccccccccchHHHHHHhhc
Q 041414 76 HECSVCGLEFAIGQALGGHMRRH 98 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~h 98 (152)
|.|+.|++.|.....|.+|++.|
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 24
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=98.25 E-value=6.4e-07 Score=64.77 Aligned_cols=72 Identities=19% Similarity=0.412 Sum_probs=51.3
Q ss_pred CCCcceecCc--ccccCCChhHHHHHHHh-cCCCCCCCCCCCCcccccccCCCCceeccccccccccchHHHHHHh
Q 041414 24 VADRAFECKT--CNRQFPSFQALGGHRAS-HKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGHMR 96 (152)
Q Consensus 24 ~~e~~~~C~~--C~k~f~~~~~L~~h~~~-h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~ 96 (152)
.++|||+|++ |.|+|.....|+.|+.- |..++..+-+.-. .+.-.....|||.|++|+|.+.....|+.|..
T Consensus 345 ~d~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~-~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 345 KDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPE-KMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred ecCceecCCCCCchhhhccccchhhhhhccccCcccCCCCCcc-ccccccccCCceeccccchhhccCccceeccc
Confidence 4579999987 99999999999999763 4333222211100 11112345799999999999999999998865
No 25
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.13 E-value=1.8e-06 Score=64.61 Aligned_cols=50 Identities=18% Similarity=0.422 Sum_probs=42.7
Q ss_pred cchhcccCCCCCCCccccccccC--------CCc-------------------------ceecCcccccCCChhHHHHHH
Q 041414 2 ANCLMFMPHGGDFDAVNGVNMAV--------ADR-------------------------AFECKTCNRQFPSFQALGGHR 48 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~~h~--------~e~-------------------------~~~C~~C~k~f~~~~~L~~h~ 48 (152)
+.|+|.|+...+|. .|.|+|. +.. -|.|.+|+|.|.....|+.|+
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 57999999999999 9999983 222 288999999999999999998
Q ss_pred HhcCC
Q 041414 49 ASHKK 53 (152)
Q Consensus 49 ~~h~~ 53 (152)
.+|..
T Consensus 377 lthq~ 381 (500)
T KOG3993|consen 377 LTHQR 381 (500)
T ss_pred Hhhhc
Confidence 88753
No 26
>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=98.11 E-value=1.7e-06 Score=38.63 Aligned_cols=23 Identities=30% Similarity=0.710 Sum_probs=21.3
Q ss_pred eecCcccccCCChhHHHHHHHhc
Q 041414 29 FECKTCNRQFPSFQALGGHRASH 51 (152)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~h~~~h 51 (152)
|.|+.|++.|.....|..|++.|
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 68999999999999999999874
No 27
>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=98.11 E-value=6.4e-06 Score=44.96 Aligned_cols=51 Identities=24% Similarity=0.494 Sum_probs=38.7
Q ss_pred ceecCcccccCCChhHHHHHHHh-cCCCCCCCCCCCCcccccccCCCCceeccccccccccchHHHHHHhhcc
Q 041414 28 AFECKTCNRQFPSFQALGGHRAS-HKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGHMRRHR 99 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~-h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~ 99 (152)
.|.|++|++. .+...|..|... |..+ .+.+.|++|...+. .+|.+|+..++
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~------------------~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSE------------------SKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCC------------------CCCccCCCchhhhh--hHHHHHHHHhc
Confidence 5899999995 556789999765 4432 35789999998655 48999998754
No 28
>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=97.99 E-value=4e-06 Score=38.96 Aligned_cols=26 Identities=38% Similarity=0.645 Sum_probs=23.8
Q ss_pred ceeccccccccccchHHHHHHhhccC
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRA 100 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~ 100 (152)
||+|..|++.|.....|..|++.|..
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 68999999999999999999998753
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=97.97 E-value=5.1e-06 Score=37.20 Aligned_cols=24 Identities=38% Similarity=0.832 Sum_probs=20.1
Q ss_pred eeccccccccccchHHHHHHhhcc
Q 041414 76 HECSVCGLEFAIGQALGGHMRRHR 99 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~h~ 99 (152)
|.|++|++.|.+...|..|+++|.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999998763
No 30
>PHA00732 hypothetical protein
Probab=97.90 E-value=8.3e-06 Score=48.00 Aligned_cols=38 Identities=24% Similarity=0.411 Sum_probs=32.7
Q ss_pred ceeccccccccccchHHHHHHhh-ccCCCcccccccccccC
Q 041414 75 THECSVCGLEFAIGQALGGHMRR-HRAGASHANEKLSAFSS 114 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~-h~~~~~~~~~~~~~~~~ 114 (152)
||.|..||+.|.+...|..|++. |.+. .+..|+++|..
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~~--~C~~CgKsF~~ 39 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTLT--KCPVCNKSYRR 39 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCCC--ccCCCCCEeCC
Confidence 68999999999999999999984 6653 46899999984
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.75 E-value=2.3e-05 Score=47.88 Aligned_cols=70 Identities=20% Similarity=0.349 Sum_probs=22.8
Q ss_pred ecCcccccCCChhHHHHHHHhcCCCCCCCCCCC-Cc----ccccccCCCCceeccccccccccchHHHHHHhhccC
Q 041414 30 ECKTCNRQFPSFQALGGHRASHKKSRVTEGSGG-GV----DTQQSPVKPKTHECSVCGLEFAIGQALGGHMRRHRA 100 (152)
Q Consensus 30 ~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~-~~----~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h~~ 100 (152)
.|..|+..|.....|..|+...++...-..... .. .+.+. .....+.|..|++.|.+...|..|++.+..
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~H 75 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRK-KVKESFRCPYCNKTFRSREALQEHMRSKHH 75 (100)
T ss_dssp -------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTTT
T ss_pred Ccccccccccccccccccccccccccccccccccccccccccccc-ccCCCCCCCccCCCCcCHHHHHHHHcCccC
Confidence 488889998888888888865433211110000 00 11111 112369999999999999999999997543
No 32
>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=97.71 E-value=1.8e-05 Score=36.68 Aligned_cols=25 Identities=44% Similarity=0.897 Sum_probs=23.0
Q ss_pred ceecCcccccCCChhHHHHHHHhcC
Q 041414 28 AFECKTCNRQFPSFQALGGHRASHK 52 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~h~ 52 (152)
||.|..|++.|.....|..|++.|.
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 6899999999999999999998774
No 33
>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=97.69 E-value=3.3e-05 Score=34.44 Aligned_cols=23 Identities=35% Similarity=0.756 Sum_probs=19.5
Q ss_pred eecCcccccCCChhHHHHHHHhc
Q 041414 29 FECKTCNRQFPSFQALGGHRASH 51 (152)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~h~~~h 51 (152)
|.|++|++.|.....|..|+.+|
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 68999999999999999999876
No 34
>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=97.69 E-value=4.1e-05 Score=40.47 Aligned_cols=32 Identities=16% Similarity=0.387 Sum_probs=23.6
Q ss_pred CCCceeccccccccccchHHHHHHhhccCCCc
Q 041414 72 KPKTHECSVCGLEFAIGQALGGHMRRHRAGAS 103 (152)
Q Consensus 72 ~~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~ 103 (152)
.+.|-.|++|+..+.+..+|++|+.++++.+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 36799999999999999999999998888765
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.56 E-value=5.6e-05 Score=34.19 Aligned_cols=25 Identities=40% Similarity=0.675 Sum_probs=22.3
Q ss_pred eeccccccccccchHHHHHHhhccC
Q 041414 76 HECSVCGLEFAIGQALGGHMRRHRA 100 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~h~~ 100 (152)
|.|..|++.|.....|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 5799999999999999999997753
No 36
>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=97.48 E-value=0.00013 Score=38.64 Aligned_cols=33 Identities=12% Similarity=0.238 Sum_probs=23.6
Q ss_pred CCCcceecCcccccCCChhHHHHHHHhcCCCCC
Q 041414 24 VADRAFECKTCNRQFPSFQALGGHRASHKKSRV 56 (152)
Q Consensus 24 ~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~ 56 (152)
..+.|..|++|+..+.+..+|.+|+.++++.+|
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 467899999999999999999999988776554
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.27 E-value=0.00025 Score=31.89 Aligned_cols=24 Identities=33% Similarity=0.693 Sum_probs=21.7
Q ss_pred eecCcccccCCChhHHHHHHHhcC
Q 041414 29 FECKTCNRQFPSFQALGGHRASHK 52 (152)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~h~~~h~ 52 (152)
|.|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 579999999999999999998764
No 38
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.07 E-value=0.00034 Score=31.62 Aligned_cols=23 Identities=26% Similarity=0.660 Sum_probs=21.0
Q ss_pred eeccccccccccchHHHHHHhhc
Q 041414 76 HECSVCGLEFAIGQALGGHMRRH 98 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~h 98 (152)
|.|.+|++.|.+...|..|++.+
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 68999999999999999999764
No 39
>PRK04860 hypothetical protein; Provisional
Probab=96.83 E-value=0.00084 Score=44.87 Aligned_cols=39 Identities=18% Similarity=0.462 Sum_probs=30.3
Q ss_pred cceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccccccc
Q 041414 27 RAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIG 88 (152)
Q Consensus 27 ~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~ 88 (152)
-+|.|. |++ ...++.+|.++|.+ +++|.|..|+..|...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g-------------------~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRG-------------------EAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcC-------------------CccEECCCCCceeEEe
Confidence 478998 887 55678888888876 6788888888887654
No 40
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.79 E-value=0.00091 Score=29.88 Aligned_cols=23 Identities=26% Similarity=0.629 Sum_probs=18.4
Q ss_pred eeccccccccccchHHHHHHhhcc
Q 041414 76 HECSVCGLEFAIGQALGGHMRRHR 99 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~h~ 99 (152)
|+|+.|+.... ...|.+|+++|.
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 78999998888 889999999865
No 41
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=96.77 E-value=0.00094 Score=50.77 Aligned_cols=56 Identities=16% Similarity=0.354 Sum_probs=49.3
Q ss_pred cchhcccCCCCCCCcccccc--ccCCC--cceecC--cccccCCChhHHHHHHHhcCCCCCCCC
Q 041414 2 ANCLMFMPHGGDFDAVNGVN--MAVAD--RAFECK--TCNRQFPSFQALGGHRASHKKSRVTEG 59 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~--~h~~e--~~~~C~--~C~k~f~~~~~L~~h~~~h~~~~~~~c 59 (152)
+.|...|+....+. .|.+ .|+++ +|+.|+ .|++.|.....+..|...|.+..+..+
T Consensus 293 ~~~~~~~s~~~~l~--~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 293 KQCNISFSRSSPLT--RHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred ccccCCcccccccc--ccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 46788898898888 9999 89999 999999 799999999999999999988766553
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.70 E-value=0.00086 Score=30.21 Aligned_cols=23 Identities=39% Similarity=0.716 Sum_probs=20.6
Q ss_pred eecCcccccCCChhHHHHHHHhc
Q 041414 29 FECKTCNRQFPSFQALGGHRASH 51 (152)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~h~~~h 51 (152)
|.|.+|++.|.+...|..|++.+
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 67999999999999999998753
No 43
>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=96.54 E-value=0.00081 Score=31.03 Aligned_cols=22 Identities=27% Similarity=0.558 Sum_probs=20.4
Q ss_pred eeccccccccccchHHHHHHhh
Q 041414 76 HECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
|.|..|++.|.....|..|++.
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 7899999999999999999875
No 44
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.35 E-value=0.0032 Score=53.86 Aligned_cols=93 Identities=17% Similarity=0.305 Sum_probs=63.6
Q ss_pred cchhcccCCCCCCCcccccc-ccCCCcceecCcccccCCChhHHHHHHHh-cCCCCCCCCCCCCcccccc------cCCC
Q 041414 2 ANCLMFMPHGGDFDAVNGVN-MAVADRAFECKTCNRQFPSFQALGGHRAS-HKKSRVTEGSGGGVDTQQS------PVKP 73 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~-~h~~e~~~~C~~C~k~f~~~~~L~~h~~~-h~~~~~~~c~~~~~~h~~~------h~~~ 73 (152)
.-|+..+.+.+.+. .|+. .|+-.+.+.|+.|+..|+....|..|||. |...+.-.|.... .|.+. -.+.
T Consensus 440 ~~~e~~~~s~r~~~--~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq-~~~~~arg~~~~~~~ 516 (1406)
T KOG1146|consen 440 TKAEPLLESKRSLE--GQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQ-NHPRLARGEVYRCPG 516 (1406)
T ss_pred cchhhhhhhhcccc--cceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcc-ccccccccccccCCC
Confidence 34555666666555 5543 46667999999999999999999999987 3221111122111 22211 1235
Q ss_pred CceeccccccccccchHHHHHHhh
Q 041414 74 KTHECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
++|.|..|..++....+|.+|++.
T Consensus 517 ~p~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 517 KPYPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred CcccceeeeeeeecchHHHHHHHH
Confidence 799999999999999999999874
No 45
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=95.92 E-value=0.006 Score=27.61 Aligned_cols=21 Identities=29% Similarity=0.618 Sum_probs=17.3
Q ss_pred eeccccccccccchHHHHHHhh
Q 041414 76 HECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
..|+.||+.| ....|.+|+.+
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 56778889764
No 46
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.80 E-value=0.0068 Score=26.92 Aligned_cols=23 Identities=22% Similarity=0.496 Sum_probs=18.0
Q ss_pred eecCcccccCCChhHHHHHHHhcC
Q 041414 29 FECKTCNRQFPSFQALGGHRASHK 52 (152)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~h~~~h~ 52 (152)
|.|+.|+.... ...|..|++.+.
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 68999998887 889999998754
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=95.59 E-value=0.0036 Score=28.79 Aligned_cols=22 Identities=36% Similarity=0.694 Sum_probs=19.6
Q ss_pred eecCcccccCCChhHHHHHHHh
Q 041414 29 FECKTCNRQFPSFQALGGHRAS 50 (152)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~h~~~ 50 (152)
|.|..|++.|.....+..|+++
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 6799999999999999988764
No 48
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=95.43 E-value=0.013 Score=35.51 Aligned_cols=24 Identities=42% Similarity=0.742 Sum_probs=21.1
Q ss_pred ceecCcccccCCChhHHHHHHHhc
Q 041414 28 AFECKTCNRQFPSFQALGGHRASH 51 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~h 51 (152)
.+.|.+|++.|.+...|..|++.+
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCccCCCCcCHHHHHHHHcCc
Confidence 589999999999999999999864
No 49
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=95.07 E-value=0.0078 Score=42.44 Aligned_cols=48 Identities=31% Similarity=0.556 Sum_probs=38.1
Q ss_pred eecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccccccchHHHHH-Hhhcc
Q 041414 29 FECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGH-MRRHR 99 (152)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H-~~~h~ 99 (152)
-+|=+|++.|....-|.+|++ .|.|+|.+|-|..-+...|..| |++|.
T Consensus 11 pwcwycnrefddekiliqhqk-----------------------akhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQK-----------------------AKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred ceeeecccccchhhhhhhhhh-----------------------hccceeeeehhhhccCCCceeehhhhhh
Confidence 468899999999988888876 5679999999877777777776 45554
No 50
>PRK04860 hypothetical protein; Provisional
Probab=94.95 E-value=0.019 Score=38.40 Aligned_cols=38 Identities=16% Similarity=0.071 Sum_probs=32.0
Q ss_pred CceeccccccccccchHHHHHHhhccCCCccc-ccccccccCC
Q 041414 74 KTHECSVCGLEFAIGQALGGHMRRHRAGASHA-NEKLSAFSSL 115 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~-~~~~~~~~~~ 115 (152)
-+|.|. |++ ....+.+|.++|+++++|. ..|+..+...
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 479998 997 7778899999999999887 6888877654
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=94.85 E-value=0.021 Score=27.70 Aligned_cols=23 Identities=17% Similarity=0.541 Sum_probs=20.6
Q ss_pred ceeccccccccccchHHHHHHhh
Q 041414 75 THECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
+|.|..|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999864
No 52
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=94.74 E-value=0.031 Score=41.15 Aligned_cols=26 Identities=27% Similarity=0.478 Sum_probs=23.3
Q ss_pred CCCceeccc--cccccccchHHHHHHhh
Q 041414 72 KPKTHECSV--CGLEFAIGQALGGHMRR 97 (152)
Q Consensus 72 ~~k~~~C~~--C~k~F~~~~~L~~H~~~ 97 (152)
++|||+|++ |.|.+.....|+.|+.-
T Consensus 346 d~KpykCpV~gC~K~YknqnGLKYH~lh 373 (423)
T COG5189 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLH 373 (423)
T ss_pred cCceecCCCCCchhhhccccchhhhhhc
Confidence 369999998 99999999999999873
No 53
>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=94.61 E-value=0.031 Score=27.08 Aligned_cols=23 Identities=30% Similarity=0.576 Sum_probs=20.1
Q ss_pred ceecCcccccCCChhHHHHHHHh
Q 041414 28 AFECKTCNRQFPSFQALGGHRAS 50 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~ 50 (152)
+|.|++|++.|.....+..|+..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 68899999999999999888753
No 54
>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=93.15 E-value=0.11 Score=28.09 Aligned_cols=35 Identities=23% Similarity=0.325 Sum_probs=24.3
Q ss_pred ceeccccccccccchHHHHHHhh-ccCCC-cc-cccccc
Q 041414 75 THECSVCGLEFAIGQALGGHMRR-HRAGA-SH-ANEKLS 110 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~-h~~~~-~~-~~~~~~ 110 (152)
.|.|++|++. .....|..|... |..+. .+ ++.|..
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchh
Confidence 4899999995 456789999765 65542 22 377764
No 55
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.99 E-value=0.055 Score=41.11 Aligned_cols=61 Identities=26% Similarity=0.412 Sum_probs=46.0
Q ss_pred ceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCC--Cceecc--ccccccccchHHHHHHhhccCCCc
Q 041414 28 AFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKP--KTHECS--VCGLEFAIGQALGGHMRRHRAGAS 103 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~--k~~~C~--~C~k~F~~~~~L~~H~~~h~~~~~ 103 (152)
++.|..|...|.....|..|.+. ..|.++ +++.|+ .|++.|.+...+.+|..+|.+..+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~-----------------~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRS-----------------VNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP 351 (467)
T ss_pred CCCCccccCCccccccccccccc-----------------cccccccCCceeeeccCCCccccccccccCCcccccCCCc
Confidence 56677777777777777666651 034446 788888 799999999999999999988775
Q ss_pred cc
Q 041414 104 HA 105 (152)
Q Consensus 104 ~~ 105 (152)
..
T Consensus 352 ~~ 353 (467)
T COG5048 352 AK 353 (467)
T ss_pred cc
Confidence 54
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=90.79 E-value=0.13 Score=27.82 Aligned_cols=28 Identities=18% Similarity=0.362 Sum_probs=24.2
Q ss_pred cCCCCceeccccccccccchHHHHHHhh
Q 041414 70 PVKPKTHECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 70 h~~~k~~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
..||.-+.|+.||..|.......+|...
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 4567889999999999999999999754
No 57
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=88.53 E-value=0.39 Score=34.35 Aligned_cols=47 Identities=19% Similarity=0.483 Sum_probs=35.3
Q ss_pred ceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccccccchHHHHHHh
Q 041414 28 AFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGHMR 96 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~ 96 (152)
-|.|.+||..... ..+.+|+-...+ .-|.|..||+.|.. -....|..
T Consensus 3 ~FtCnvCgEsvKK-p~vekH~srCrn--------------------~~fSCIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 3 FFTCNVCGESVKK-PQVEKHMSRCRN--------------------AYFSCIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred EEehhhhhhhccc-cchHHHHHhccC--------------------CeeEEeeccccccc-chhhhhhh
Confidence 3789999998764 557778765443 36999999999998 45667765
No 58
>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=86.83 E-value=0.47 Score=22.79 Aligned_cols=10 Identities=40% Similarity=0.973 Sum_probs=7.7
Q ss_pred Cceecccccc
Q 041414 74 KTHECSVCGL 83 (152)
Q Consensus 74 k~~~C~~C~k 83 (152)
.++.|+.||.
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4788888874
No 59
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=86.79 E-value=0.61 Score=24.65 Aligned_cols=24 Identities=29% Similarity=0.728 Sum_probs=19.1
Q ss_pred eeccccccccccc-----hHHHHHHh-hcc
Q 041414 76 HECSVCGLEFAIG-----QALGGHMR-RHR 99 (152)
Q Consensus 76 ~~C~~C~k~F~~~-----~~L~~H~~-~h~ 99 (152)
-.|..|++.+... ++|.+|++ +|.
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~ 48 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHP 48 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCc
Confidence 5699999988665 69999998 564
No 60
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=86.71 E-value=0.22 Score=35.06 Aligned_cols=20 Identities=20% Similarity=0.659 Sum_probs=15.5
Q ss_pred CcceecCcccccCCChhHHH
Q 041414 26 DRAFECKTCNRQFPSFQALG 45 (152)
Q Consensus 26 e~~~~C~~C~k~f~~~~~L~ 45 (152)
++...|++|++.|..+.-..
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs 22 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRS 22 (214)
T ss_pred CCceECCCCCCeeeeeEEEc
Confidence 46789999999998774333
No 61
>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=85.75 E-value=0.48 Score=30.67 Aligned_cols=30 Identities=30% Similarity=0.571 Sum_probs=19.0
Q ss_pred CCceeccccccccccchHHHHHHhhccCCCccc
Q 041414 73 PKTHECSVCGLEFAIGQALGGHMRRHRAGASHA 105 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~ 105 (152)
+..-.|-+||+.|.. |++|++.|.|-.+..
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp~e 99 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTPEE 99 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-HHH
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCHHH
Confidence 445789999999987 589999997766543
No 62
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=85.39 E-value=0.22 Score=40.80 Aligned_cols=28 Identities=29% Similarity=0.511 Sum_probs=24.8
Q ss_pred CceeccccccccccchHHHHHHhhccCC
Q 041414 74 KTHECSVCGLEFAIGQALGGHMRRHRAG 101 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L~~H~~~h~~~ 101 (152)
-.|.|.+|+|+|-....++.||++|.-.
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q 818 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQ 818 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHH
Confidence 3599999999999999999999999643
No 63
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=84.06 E-value=0.53 Score=41.11 Aligned_cols=70 Identities=24% Similarity=0.429 Sum_probs=45.4
Q ss_pred CcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccccccchHHHHHHhhc
Q 041414 26 DRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGHMRRH 98 (152)
Q Consensus 26 e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~~~h 98 (152)
..+|.|..|...|.....|..|++.- .+-.+.......+...+....+| |..|...|.....|..||++-
T Consensus 1282 ~~~~~~~~~~~~~~~~~~l~~~~~k~--~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~~~~~alqihm~~~ 1351 (1406)
T KOG1146|consen 1282 THRYLCRQCKMAFDGEAPLTAHQRKF--CFAGRGSGGSMPPPLRVPDCTYH-CLACEVLLSGREALQIHMRSS 1351 (1406)
T ss_pred chhHHHHHHHhhhcchhHHHHHHHHH--HhccCccccCCCCcccCcccccc-chHHHhhcchhHHHHHHHHHh
Confidence 34677777877777777777776211 00011111111344455556678 999999999999999999863
No 64
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=83.73 E-value=0.59 Score=25.32 Aligned_cols=32 Identities=13% Similarity=0.199 Sum_probs=26.2
Q ss_pred cccCCCcceecCcccccCCChhHHHHHHHhcC
Q 041414 21 NMAVADRAFECKTCNRQFPSFQALGGHRASHK 52 (152)
Q Consensus 21 ~~h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~ 52 (152)
...-||.-+.|+-||..|....++.+|....+
T Consensus 10 ~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 10 RDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred eccCCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 34567888999999999999999999976433
No 65
>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=83.59 E-value=1.1 Score=22.85 Aligned_cols=24 Identities=25% Similarity=0.574 Sum_probs=16.0
Q ss_pred CCceeccccccccccc----hHHHHHHh
Q 041414 73 PKTHECSVCGLEFAIG----QALGGHMR 96 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~----~~L~~H~~ 96 (152)
.....|..|++.+... +.|.+|++
T Consensus 14 ~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 14 KKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp SS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred cCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 4567899999988764 78999984
No 66
>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=83.08 E-value=0.94 Score=20.51 Aligned_cols=20 Identities=25% Similarity=0.517 Sum_probs=15.8
Q ss_pred eeccccccccccchHHHHHHh
Q 041414 76 HECSVCGLEFAIGQALGGHMR 96 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~ 96 (152)
..|++|++.+ ....++.|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999998 5577888875
No 67
>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=81.12 E-value=0.9 Score=28.37 Aligned_cols=15 Identities=33% Similarity=0.689 Sum_probs=12.7
Q ss_pred Cceeccccccccccc
Q 041414 74 KTHECSVCGLEFAIG 88 (152)
Q Consensus 74 k~~~C~~C~k~F~~~ 88 (152)
.|-.|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 578899999999876
No 68
>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=78.57 E-value=1.5 Score=21.24 Aligned_cols=10 Identities=30% Similarity=1.105 Sum_probs=7.0
Q ss_pred Cceecccccc
Q 041414 74 KTHECSVCGL 83 (152)
Q Consensus 74 k~~~C~~C~k 83 (152)
.|..|++||.
T Consensus 17 ~p~~CP~Cg~ 26 (34)
T cd00729 17 APEKCPICGA 26 (34)
T ss_pred CCCcCcCCCC
Confidence 4667888874
No 69
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.66 E-value=2.3 Score=23.42 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=8.6
Q ss_pred CCceecccccc
Q 041414 73 PKTHECSVCGL 83 (152)
Q Consensus 73 ~k~~~C~~C~k 83 (152)
..+|.|+.||.
T Consensus 48 g~~Y~Cp~CGF 58 (61)
T COG2888 48 GNPYRCPKCGF 58 (61)
T ss_pred CCceECCCcCc
Confidence 45899999984
No 70
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=76.27 E-value=1.5 Score=22.69 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=8.4
Q ss_pred ceeccccccccc
Q 041414 75 THECSVCGLEFA 86 (152)
Q Consensus 75 ~~~C~~C~k~F~ 86 (152)
...|+.||..+.
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 578888886544
No 71
>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=76.18 E-value=1.1 Score=22.01 Aligned_cols=14 Identities=21% Similarity=0.774 Sum_probs=10.5
Q ss_pred eecCcccccCCChh
Q 041414 29 FECKTCNRQFPSFQ 42 (152)
Q Consensus 29 ~~C~~C~k~f~~~~ 42 (152)
..|+.|+..|.-..
T Consensus 3 ~~CP~C~~~~~v~~ 16 (38)
T TIGR02098 3 IQCPNCKTSFRVVD 16 (38)
T ss_pred EECCCCCCEEEeCH
Confidence 57888988887554
No 72
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=74.88 E-value=9.2 Score=24.05 Aligned_cols=74 Identities=15% Similarity=0.107 Sum_probs=43.8
Q ss_pred CcceecCcccccCCChhHHHHHHHhcCCCCCC------------CCCCCCcccccc-------cCCCCceeccccccccc
Q 041414 26 DRAFECKTCNRQFPSFQALGGHRASHKKSRVT------------EGSGGGVDTQQS-------PVKPKTHECSVCGLEFA 86 (152)
Q Consensus 26 e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~------------~c~~~~~~h~~~-------h~~~k~~~C~~C~k~F~ 86 (152)
+-|-+|++||-.......|.+--..--.-++| .|..|....... -.....|+|+.|...|-
T Consensus 13 ~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC 92 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFC 92 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccc
Confidence 45788999999998888888632110111111 133333211100 11233588999999888
Q ss_pred cchHHHHHHhhcc
Q 041414 87 IGQALGGHMRRHR 99 (152)
Q Consensus 87 ~~~~L~~H~~~h~ 99 (152)
..-..-.|...|.
T Consensus 93 ~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 93 VDCDVFVHESLHC 105 (112)
T ss_pred cccchhhhhhccC
Confidence 8877777877765
No 73
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=74.39 E-value=2.8 Score=24.97 Aligned_cols=31 Identities=23% Similarity=0.338 Sum_probs=19.4
Q ss_pred CCCCCCCCc-ccccccCCCCceeccccccccccc
Q 041414 56 VTEGSGGGV-DTQQSPVKPKTHECSVCGLEFAIG 88 (152)
Q Consensus 56 ~~~c~~~~~-~h~~~h~~~k~~~C~~C~k~F~~~ 88 (152)
.+.|+.|+. .+.+.-+ ..|.|.-||..|.-.
T Consensus 35 ~~~Cp~C~~~~VkR~a~--GIW~C~kCg~~fAGg 66 (89)
T COG1997 35 KHVCPFCGRTTVKRIAT--GIWKCRKCGAKFAGG 66 (89)
T ss_pred CCcCCCCCCcceeeecc--CeEEcCCCCCeeccc
Confidence 455666655 3333333 369999999998754
No 74
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=73.98 E-value=0.76 Score=32.71 Aligned_cols=42 Identities=24% Similarity=0.391 Sum_probs=29.4
Q ss_pred CCCCCccccccccCCCcceecCcccccCCChhHHHHH-HHhcC
Q 041414 11 GGDFDAVNGVNMAVADRAFECKTCNRQFPSFQALGGH-RASHK 52 (152)
Q Consensus 11 ~~~~~~~~h~~~h~~e~~~~C~~C~k~f~~~~~L~~h-~~~h~ 52 (152)
.++|++..-+..|...|-|+|.+|.|.+-+-..|..| |++|.
T Consensus 17 nrefddekiliqhqkakhfkchichkkl~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 17 NREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHK 59 (341)
T ss_pred ccccchhhhhhhhhhhccceeeeehhhhccCCCceeehhhhhh
Confidence 3445543333346667889999999998888888887 55663
No 75
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=73.08 E-value=3 Score=20.50 Aligned_cols=14 Identities=29% Similarity=0.726 Sum_probs=10.3
Q ss_pred CCceeccccccccc
Q 041414 73 PKTHECSVCGLEFA 86 (152)
Q Consensus 73 ~k~~~C~~C~k~F~ 86 (152)
.+..+|+.|+..|.
T Consensus 23 ~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 23 GRKVRCPKCGHVFR 36 (37)
T ss_pred CcEEECCCCCcEee
Confidence 34678888887774
No 76
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=72.65 E-value=2.6 Score=27.74 Aligned_cols=18 Identities=11% Similarity=0.674 Sum_probs=13.0
Q ss_pred CCcceecCcccccCCChh
Q 041414 25 ADRAFECKTCNRQFPSFQ 42 (152)
Q Consensus 25 ~e~~~~C~~C~k~f~~~~ 42 (152)
+..-|.|+.|+..|....
T Consensus 96 ~~~~Y~Cp~C~~~y~~~e 113 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLE 113 (147)
T ss_pred CCcEEECcCCCCEeeHHH
Confidence 445688999998887543
No 77
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=70.71 E-value=2.3 Score=27.54 Aligned_cols=27 Identities=22% Similarity=0.249 Sum_probs=21.9
Q ss_pred ceeccccccccccchHHHHHHhhccCCCcc
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRAGASH 104 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~ 104 (152)
-..|-++|+.|.+ |++|+.+|.|-.|.
T Consensus 76 ~IicLEDGkkfKS---LKRHL~t~~gmTPd 102 (148)
T COG4957 76 YIICLEDGKKFKS---LKRHLTTHYGLTPD 102 (148)
T ss_pred eEEEeccCcchHH---HHHHHhcccCCCHH
Confidence 3569999999985 89999999876553
No 78
>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=70.71 E-value=3.1 Score=27.84 Aligned_cols=21 Identities=19% Similarity=0.295 Sum_probs=14.0
Q ss_pred CCCcceecCcccccCCChhHH
Q 041414 24 VADRAFECKTCNRQFPSFQAL 44 (152)
Q Consensus 24 ~~e~~~~C~~C~k~f~~~~~L 44 (152)
++..-|.|+.|+..|+....+
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHH
Confidence 344567788888777766554
No 79
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=69.85 E-value=1.4 Score=33.17 Aligned_cols=69 Identities=20% Similarity=0.369 Sum_probs=41.0
Q ss_pred CcceecCc--ccccCCChhHHHHHHHhcCCCCCCC-CCCCCcccccccCCCCceeccccccccccchHHHHHH
Q 041414 26 DRAFECKT--CNRQFPSFQALGGHRASHKKSRVTE-GSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGHM 95 (152)
Q Consensus 26 e~~~~C~~--C~k~f~~~~~L~~h~~~h~~~~~~~-c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H~ 95 (152)
.++|+|.+ |.+.+.....|+.|...-+.. +.. ...-..-|.-.....|+|+|++|.+.+.....|+.|.
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s-~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCS-PITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCC-CCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 46788854 888888777777664321110 000 0001113444445579999999998888776665543
No 80
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=69.78 E-value=4 Score=22.47 Aligned_cols=11 Identities=27% Similarity=0.887 Sum_probs=8.5
Q ss_pred CCceecccccc
Q 041414 73 PKTHECSVCGL 83 (152)
Q Consensus 73 ~k~~~C~~C~k 83 (152)
..+|.|+.||.
T Consensus 46 ~~~Y~CP~CGF 56 (59)
T PRK14890 46 SNPYTCPKCGF 56 (59)
T ss_pred CCceECCCCCC
Confidence 35799999984
No 81
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=68.94 E-value=3.2 Score=28.35 Aligned_cols=20 Identities=25% Similarity=0.516 Sum_probs=13.3
Q ss_pred CCcceecCcccccCCChhHH
Q 041414 25 ADRAFECKTCNRQFPSFQAL 44 (152)
Q Consensus 25 ~e~~~~C~~C~k~f~~~~~L 44 (152)
+..-|.|+.|+..|+....+
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAM 133 (178)
T ss_pred CCCEEECCCCCcEEeHHHHh
Confidence 34567888888887765543
No 82
>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=68.44 E-value=4.1 Score=25.24 Aligned_cols=70 Identities=14% Similarity=0.263 Sum_probs=43.7
Q ss_pred cceecCcccccCCChhHHHHHHHh-cCCCCC------------CC---CCC-------CCc---ccccccCCCCceec--
Q 041414 27 RAFECKTCNRQFPSFQALGGHRAS-HKKSRV------------TE---GSG-------GGV---DTQQSPVKPKTHEC-- 78 (152)
Q Consensus 27 ~~~~C~~C~k~f~~~~~L~~h~~~-h~~~~~------------~~---c~~-------~~~---~h~~~h~~~k~~~C-- 78 (152)
+-..|..|+-+... +.+..|.+. |..... +. ... -.. ..+.++ .-|.|
T Consensus 10 ~vlIC~~C~~av~~-~~v~~HL~~~H~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~p~~~~~Pi~gLp~~---~G~~C~~ 85 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-SEVESHLRKRHHILKSQERQRIVEAIRQWPDLLPDPDDLQIPPDPSPPIPGLPVY---DGYRCQC 85 (109)
T ss_pred CEEEeCCCCcccCc-hHHHHHHHHhcccccHHHHHHHHHHHHhhhhcccCccccCCCCCCCCcCCCCCCC---CCeeeec
Confidence 45678899887765 778888874 322111 00 000 000 222222 34899
Q ss_pred --cccccccccchHHHHHHhhccC
Q 041414 79 --SVCGLEFAIGQALGGHMRRHRA 100 (152)
Q Consensus 79 --~~C~k~F~~~~~L~~H~~~h~~ 100 (152)
..|+..+.+...+.+|++.++|
T Consensus 86 ~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 86 DPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCCCCCcEeccHHHHHHHHHHhcC
Confidence 9999999999999999987654
No 83
>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=67.98 E-value=3.4 Score=26.50 Aligned_cols=20 Identities=20% Similarity=0.243 Sum_probs=14.7
Q ss_pred CCceeccccccccccchHHH
Q 041414 73 PKTHECSVCGLEFAIGQALG 92 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~ 92 (152)
..|-.|+.||..|.....++
T Consensus 24 k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 24 RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred CCCccCCCcCCccCcchhhc
Confidence 35788999999987664444
No 84
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=67.49 E-value=3.9 Score=21.06 Aligned_cols=13 Identities=23% Similarity=0.636 Sum_probs=9.6
Q ss_pred ceecCcccccCCC
Q 041414 28 AFECKTCNRQFPS 40 (152)
Q Consensus 28 ~~~C~~C~k~f~~ 40 (152)
.|.|..||..|..
T Consensus 2 ~Y~C~~Cg~~~~~ 14 (44)
T smart00659 2 IYICGECGRENEI 14 (44)
T ss_pred EEECCCCCCEeec
Confidence 3788888887753
No 85
>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=66.98 E-value=4.3 Score=28.62 Aligned_cols=29 Identities=14% Similarity=0.368 Sum_probs=22.2
Q ss_pred CCCcceecCcccccCCChhHHHHHHHhcC
Q 041414 24 VADRAFECKTCNRQFPSFQALGGHRASHK 52 (152)
Q Consensus 24 ~~e~~~~C~~C~k~f~~~~~L~~h~~~h~ 52 (152)
.++..|.|..|+|.|.-...+..|+..-+
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 45667999999999999999999987643
No 86
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=65.88 E-value=1.2 Score=36.72 Aligned_cols=26 Identities=23% Similarity=0.694 Sum_probs=23.3
Q ss_pred ceecCcccccCCChhHHHHHHHhcCC
Q 041414 28 AFECKTCNRQFPSFQALGGHRASHKK 53 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~h~~ 53 (152)
-|.|.+|+|.|-...++..||++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 38999999999999999999999853
No 87
>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=65.46 E-value=5 Score=26.41 Aligned_cols=22 Identities=18% Similarity=0.314 Sum_probs=17.5
Q ss_pred CCceeccccccccccchHHHHH
Q 041414 73 PKTHECSVCGLEFAIGQALGGH 94 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~~H 94 (152)
+.-|.|+.||+.|...++..+-
T Consensus 122 ~~f~~C~~C~kiyW~GsH~~~~ 143 (147)
T PF01927_consen 122 DEFWRCPGCGKIYWEGSHWRRM 143 (147)
T ss_pred CeEEECCCCCCEecccccHHHH
Confidence 3468999999999988876543
No 88
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=65.10 E-value=4.8 Score=26.85 Aligned_cols=18 Identities=28% Similarity=0.691 Sum_probs=13.9
Q ss_pred CceeccccccccccchHH
Q 041414 74 KTHECSVCGLEFAIGQAL 91 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L 91 (152)
+.+.|+.||+.|.....+
T Consensus 27 ~~~~c~~c~~~f~~~e~~ 44 (154)
T PRK00464 27 RRRECLACGKRFTTFERV 44 (154)
T ss_pred eeeeccccCCcceEeEec
Confidence 348999999999876544
No 89
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=63.91 E-value=4.3 Score=29.27 Aligned_cols=40 Identities=23% Similarity=0.359 Sum_probs=33.6
Q ss_pred ceeccccccccccchHHHHHHhhccCCCcccccccccccCC
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRAGASHANEKLSAFSSL 115 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~~~~ 115 (152)
-|.|..||.... +..+.+|+-.-++....+-.|+..|...
T Consensus 3 ~FtCnvCgEsvK-Kp~vekH~srCrn~~fSCIDC~k~F~~~ 42 (276)
T KOG2186|consen 3 FFTCNVCGESVK-KPQVEKHMSRCRNAYFSCIDCGKTFERV 42 (276)
T ss_pred EEehhhhhhhcc-ccchHHHHHhccCCeeEEeecccccccc
Confidence 488999998876 4568889999888888789999999884
No 90
>PHA00626 hypothetical protein
Probab=63.71 E-value=6.9 Score=21.29 Aligned_cols=15 Identities=20% Similarity=0.417 Sum_probs=12.1
Q ss_pred Cceeccccccccccc
Q 041414 74 KTHECSVCGLEFAIG 88 (152)
Q Consensus 74 k~~~C~~C~k~F~~~ 88 (152)
..|+|+.||..|+..
T Consensus 22 nrYkCkdCGY~ft~~ 36 (59)
T PHA00626 22 DDYVCCDCGYNDSKD 36 (59)
T ss_pred cceEcCCCCCeechh
Confidence 469999999888743
No 91
>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=63.52 E-value=3.3 Score=18.40 Aligned_cols=10 Identities=30% Similarity=0.919 Sum_probs=8.0
Q ss_pred Cceecccccc
Q 041414 74 KTHECSVCGL 83 (152)
Q Consensus 74 k~~~C~~C~k 83 (152)
..|.|+.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4699999984
No 92
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=62.43 E-value=6 Score=19.77 Aligned_cols=18 Identities=33% Similarity=0.444 Sum_probs=11.0
Q ss_pred ccccCCCCceeccccccc
Q 041414 67 QQSPVKPKTHECSVCGLE 84 (152)
Q Consensus 67 ~~~h~~~k~~~C~~C~k~ 84 (152)
.....+.+.|.|..|+..
T Consensus 16 ~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 16 CQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp SEEETTTTEEEETTT--E
T ss_pred ceEcCCCCEEECcCCCCc
Confidence 334445678999999864
No 93
>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=62.35 E-value=3.6 Score=20.33 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=19.5
Q ss_pred ceeccccccccccchHHHHHHhhccCCCcccccccc
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRAGASHANEKLS 110 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~ 110 (152)
.|+|..||..|...... ..++...++.|+.
T Consensus 5 ~y~C~~Cg~~fe~~~~~------~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKI------SDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEec------CCCCCCCCCCCCC
Confidence 48999999988754332 1244555577765
No 94
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.32 E-value=9.3 Score=31.59 Aligned_cols=25 Identities=24% Similarity=0.331 Sum_probs=15.9
Q ss_pred eccccccccccchHHHHHHhhccCC
Q 041414 77 ECSVCGLEFAIGQALGGHMRRHRAG 101 (152)
Q Consensus 77 ~C~~C~k~F~~~~~L~~H~~~h~~~ 101 (152)
.|..|..-|-....|.+|++.++..
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~~ 208 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHEF 208 (669)
T ss_pred cchhhhhhhccHHHHHHhhccceeh
Confidence 4666666677677777777654443
No 95
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=61.01 E-value=3.7 Score=26.59 Aligned_cols=20 Identities=15% Similarity=0.476 Sum_probs=14.3
Q ss_pred ccCCCcceecCcccccCCCh
Q 041414 22 MAVADRAFECKTCNRQFPSF 41 (152)
Q Consensus 22 ~h~~e~~~~C~~C~k~f~~~ 41 (152)
+-++.+-|+|++|..+....
T Consensus 74 vF~d~~lYeCnIC~etS~ee 93 (140)
T PF05290_consen 74 VFLDPKLYECNICKETSAEE 93 (140)
T ss_pred eecCCCceeccCcccccchh
Confidence 34566789999998876543
No 96
>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=59.89 E-value=4.2 Score=20.61 Aligned_cols=30 Identities=27% Similarity=0.406 Sum_probs=19.1
Q ss_pred ceeccccccccccchHHHHHHhhccCCCcccccccc
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRAGASHANEKLS 110 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~ 110 (152)
.|.|..||..|.....+ .......++.|+.
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSI------SEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEc------CCCCCCcCCCCCC
Confidence 48999999999865432 2234444566664
No 97
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=59.60 E-value=5.4 Score=26.94 Aligned_cols=23 Identities=22% Similarity=0.351 Sum_probs=14.0
Q ss_pred CCCCCCCCcccccccCCCCceeccccc
Q 041414 56 VTEGSGGGVDTQQSPVKPKTHECSVCG 82 (152)
Q Consensus 56 ~~~c~~~~~~h~~~h~~~k~~~C~~C~ 82 (152)
.|.|..|+..+ .|+-|..||+||
T Consensus 134 ~~vC~vCGy~~----~ge~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTH----EGEAPEVCPICG 156 (166)
T ss_pred EEEcCCCCCcc----cCCCCCcCCCCC
Confidence 35566555432 346677888887
No 98
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=59.41 E-value=6 Score=22.78 Aligned_cols=19 Identities=21% Similarity=0.602 Sum_probs=14.4
Q ss_pred CCceecc--ccccccccchHH
Q 041414 73 PKTHECS--VCGLEFAIGQAL 91 (152)
Q Consensus 73 ~k~~~C~--~C~k~F~~~~~L 91 (152)
++-+.|. .||..|.....+
T Consensus 25 ~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred eeeeecCCCCCCCEEEEEEEE
Confidence 5678898 899999875443
No 99
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=59.32 E-value=5.7 Score=28.81 Aligned_cols=76 Identities=24% Similarity=0.334 Sum_probs=44.8
Q ss_pred cCCCcceecCcccccCCChhHHHHHHHhc--CCCCCCCCCCCCc---------------ccccc----cCCCCceecccc
Q 041414 23 AVADRAFECKTCNRQFPSFQALGGHRASH--KKSRVTEGSGGGV---------------DTQQS----PVKPKTHECSVC 81 (152)
Q Consensus 23 h~~e~~~~C~~C~k~f~~~~~L~~h~~~h--~~~~~~~c~~~~~---------------~h~~~----h~~~k~~~C~~C 81 (152)
..|.+-|.|..|...+-....+ .|+..- .....|+|..|.. .|.+. ....+++.|+.|
T Consensus 137 ~hGGrif~CsfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKC 215 (314)
T PF06524_consen 137 DHGGRIFKCSFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKC 215 (314)
T ss_pred cCCCeEEEeecCCCeeeccchh-hhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCC
Confidence 3467889999998765544333 355432 1223455544432 34332 234578999999
Q ss_pred ccccccchHHHHHHhhcc
Q 041414 82 GLEFAIGQALGGHMRRHR 99 (152)
Q Consensus 82 ~k~F~~~~~L~~H~~~h~ 99 (152)
|........|..-.++|.
T Consensus 216 g~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 216 GYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCcccccccceeeeecch
Confidence 987777777765555553
No 100
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=58.51 E-value=5.4 Score=30.46 Aligned_cols=70 Identities=24% Similarity=0.401 Sum_probs=43.8
Q ss_pred ceecCcccccCCChhHHHHHHHh--cC---CCCCCCCC-----CCCcccc--------cccCCCCceeccccccccccch
Q 041414 28 AFECKTCNRQFPSFQALGGHRAS--HK---KSRVTEGS-----GGGVDTQ--------QSPVKPKTHECSVCGLEFAIGQ 89 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~--h~---~~~~~~c~-----~~~~~h~--------~~h~~~k~~~C~~C~k~F~~~~ 89 (152)
-|+|.-|...|.....-+.|.++ |. ..+...=+ .+...+. ..-.++-++.|..|.+.|....
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 37899999999988777777764 21 11111000 0000010 0123455799999999999999
Q ss_pred HHHHHHhh
Q 041414 90 ALGGHMRR 97 (152)
Q Consensus 90 ~L~~H~~~ 97 (152)
.-..|++.
T Consensus 83 a~~~hl~S 90 (390)
T KOG2785|consen 83 AHENHLKS 90 (390)
T ss_pred hHHHHHHH
Confidence 98889864
No 101
>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=58.38 E-value=4.5 Score=18.28 Aligned_cols=11 Identities=36% Similarity=1.041 Sum_probs=8.4
Q ss_pred eeccccccccc
Q 041414 76 HECSVCGLEFA 86 (152)
Q Consensus 76 ~~C~~C~k~F~ 86 (152)
-.|+.||..|.
T Consensus 15 ~~Cp~CG~~F~ 25 (26)
T PF10571_consen 15 KFCPHCGYDFE 25 (26)
T ss_pred CcCCCCCCCCc
Confidence 46888888875
No 102
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=56.70 E-value=14 Score=28.30 Aligned_cols=68 Identities=18% Similarity=0.215 Sum_probs=46.0
Q ss_pred cceecCcccccCCChhHHHHHHHhcCCCCC----CCCCCCCcccccccCC---CCceeccccc---cccccchHHHHHHh
Q 041414 27 RAFECKTCNRQFPSFQALGGHRASHKKSRV----TEGSGGGVDTQQSPVK---PKTHECSVCG---LEFAIGQALGGHMR 96 (152)
Q Consensus 27 ~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~----~~c~~~~~~h~~~h~~---~k~~~C~~C~---k~F~~~~~L~~H~~ 96 (152)
-|-.|-.|++.+..-..-..||..++|-.- |.-+.-+ +....| ..-|.|-.|+ +.|.+....+.||.
T Consensus 165 ~Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~G---Ll~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 165 IPTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKG---LLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred CCcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhH---HHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 467899999999988888889988877321 1100000 000111 2358899998 99999999999996
Q ss_pred h
Q 041414 97 R 97 (152)
Q Consensus 97 ~ 97 (152)
.
T Consensus 242 ~ 242 (390)
T KOG2785|consen 242 D 242 (390)
T ss_pred h
Confidence 3
No 103
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=56.48 E-value=4.7 Score=24.27 Aligned_cols=15 Identities=27% Similarity=0.423 Sum_probs=12.2
Q ss_pred Cceeccccccccccc
Q 041414 74 KTHECSVCGLEFAIG 88 (152)
Q Consensus 74 k~~~C~~C~k~F~~~ 88 (152)
-.|.|..|++.|.-.
T Consensus 53 GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 53 GIWRCKGCKKTVAGG 67 (90)
T ss_pred EEEEcCCCCCEEeCC
Confidence 479999999998753
No 104
>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=56.11 E-value=4.4 Score=28.56 Aligned_cols=25 Identities=20% Similarity=0.425 Sum_probs=20.0
Q ss_pred CCceeccccccccccchHHHHHHhh
Q 041414 73 PKTHECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
+.-|.|..|+|.|.-..-...|+..
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~n 99 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFN 99 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhh
Confidence 4569999999999999999999875
No 105
>PF15269 zf-C2H2_7: Zinc-finger
Probab=56.10 E-value=8.3 Score=19.92 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=18.0
Q ss_pred eeccccccccccchHHHHHHhh
Q 041414 76 HECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
|+|-.|..+-..++.|-.||+-
T Consensus 21 ykcfqcpftc~~kshl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHHHHHHHHHH
Confidence 6788888777888999999874
No 106
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=55.53 E-value=3.6 Score=28.74 Aligned_cols=84 Identities=21% Similarity=0.377 Sum_probs=51.5
Q ss_pred cchhcccCCCCCCCccccccccCCCcceecCcccccCCChhHHHHHHHh-cCCCCCCCCCCCCcccccccCCCCceeccc
Q 041414 2 ANCLMFMPHGGDFDAVNGVNMAVADRAFECKTCNRQFPSFQALGGHRAS-HKKSRVTEGSGGGVDTQQSPVKPKTHECSV 80 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~~h~~e~~~~C~~C~k~f~~~~~L~~h~~~-h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~ 80 (152)
|.|-..|.....+. .|..+- ....|.+|.+.|.+..-|..|+.- |..- | ...+-.|.--|+|-+
T Consensus 85 agc~~~~d~lD~~E--~hY~~~---h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~--F--------qa~veRG~dMy~Clv 149 (253)
T KOG4173|consen 85 AGCCQVFDALDDYE--HHYHTL---HGNSCSFCKRAFPTGHLLDAHILEWHDSL--F--------QALVERGQDMYQCLV 149 (253)
T ss_pred cchHHHHhhhhhHH--Hhhhhc---ccchhHHHHHhCCchhhhhHHHHHHHHHH--H--------HHHHHcCccHHHHHH
Confidence 44555565555554 332221 124799999999998888888742 3210 0 001122334588854
Q ss_pred --cccccccchHHHHHHh-hccC
Q 041414 81 --CGLEFAIGQALGGHMR-RHRA 100 (152)
Q Consensus 81 --C~k~F~~~~~L~~H~~-~h~~ 100 (152)
|+..|.+....+.|+- +|.-
T Consensus 150 EgCt~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 150 EGCTEKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred HhhhhhhhhhhhhhhHHHHhccC
Confidence 9999999999999974 4643
No 107
>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=53.74 E-value=6.7 Score=23.99 Aligned_cols=19 Identities=16% Similarity=0.426 Sum_probs=14.8
Q ss_pred cccCCCcceecCcccccCCC
Q 041414 21 NMAVADRAFECKTCNRQFPS 40 (152)
Q Consensus 21 ~~h~~e~~~~C~~C~k~f~~ 40 (152)
..+.| +|+.|.+||..|.-
T Consensus 73 ~l~~g-~~~rC~eCG~~fkL 91 (97)
T cd00924 73 WLEKG-KPKRCPECGHVFKL 91 (97)
T ss_pred EEeCC-CceeCCCCCcEEEE
Confidence 34556 79999999998863
No 108
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=52.63 E-value=7 Score=19.48 Aligned_cols=14 Identities=29% Similarity=0.567 Sum_probs=12.0
Q ss_pred ceeccccccccccc
Q 041414 75 THECSVCGLEFAIG 88 (152)
Q Consensus 75 ~~~C~~C~k~F~~~ 88 (152)
||+|..|++.|-..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 89999999998753
No 109
>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=52.01 E-value=3.9 Score=24.60 Aligned_cols=13 Identities=38% Similarity=0.815 Sum_probs=10.7
Q ss_pred ceecccccccccc
Q 041414 75 THECSVCGLEFAI 87 (152)
Q Consensus 75 ~~~C~~C~k~F~~ 87 (152)
.|.|..|++.|.-
T Consensus 53 IW~C~~C~~~~AG 65 (90)
T PF01780_consen 53 IWKCKKCGKKFAG 65 (90)
T ss_dssp EEEETTTTEEEE-
T ss_pred EeecCCCCCEEeC
Confidence 5999999999864
No 110
>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=51.20 E-value=14 Score=22.78 Aligned_cols=25 Identities=16% Similarity=0.357 Sum_probs=21.9
Q ss_pred eec----CcccccCCChhHHHHHHHhcCC
Q 041414 29 FEC----KTCNRQFPSFQALGGHRASHKK 53 (152)
Q Consensus 29 ~~C----~~C~k~f~~~~~L~~h~~~h~~ 53 (152)
|.| ..|+....+...|..|.+.++|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999887653
No 111
>PLN02294 cytochrome c oxidase subunit Vb
Probab=50.95 E-value=8.2 Score=26.14 Aligned_cols=20 Identities=30% Similarity=0.509 Sum_probs=15.0
Q ss_pred cccCCCCceeccccccccccc
Q 041414 68 QSPVKPKTHECSVCGLEFAIG 88 (152)
Q Consensus 68 ~~h~~~k~~~C~~C~k~F~~~ 88 (152)
..+.| +|+.|++||..|.-.
T Consensus 135 ~L~kG-kp~RCpeCG~~fkL~ 154 (174)
T PLN02294 135 WLEKG-KSFECPVCTQYFELE 154 (174)
T ss_pred EecCC-CceeCCCCCCEEEEE
Confidence 34444 699999999998743
No 112
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.32 E-value=7.5 Score=24.26 Aligned_cols=15 Identities=7% Similarity=0.051 Sum_probs=12.2
Q ss_pred CCceecccccccccc
Q 041414 73 PKTHECSVCGLEFAI 87 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~ 87 (152)
..|-.|+.||++|..
T Consensus 24 rdPiVsPytG~s~P~ 38 (129)
T COG4530 24 RDPIVSPYTGKSYPR 38 (129)
T ss_pred CCccccCcccccchH
Confidence 458889999999954
No 113
>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=50.11 E-value=7.4 Score=20.44 Aligned_cols=30 Identities=20% Similarity=0.359 Sum_probs=19.0
Q ss_pred ceeccccccccccchHHHHHHhhccCCCcccccccc
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRAGASHANEKLS 110 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~ 110 (152)
-|.|..||..|.....+ .......++.|+.
T Consensus 5 ey~C~~Cg~~fe~~~~~------~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKM------SDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEec------CCCCCCCCCCCCC
Confidence 48999999999854322 1133444577775
No 114
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=49.39 E-value=47 Score=25.40 Aligned_cols=69 Identities=20% Similarity=0.277 Sum_probs=42.8
Q ss_pred ecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc-ccc--------cccCCCCceeccc--c--c--cccccchHHHHH
Q 041414 30 ECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV-DTQ--------QSPVKPKTHECSV--C--G--LEFAIGQALGGH 94 (152)
Q Consensus 30 ~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~-~h~--------~~h~~~k~~~C~~--C--~--k~F~~~~~L~~H 94 (152)
.|..|...|-....|..|++..+. +-+.|+.-.. .|+ ..|-..-.|.|.+ | | ..|.....|..|
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~~HE-~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy~ct~qtc~~~k~~vf~~~~el~~h 300 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRLRHE-ACHICDMVGPIRYQYFKSYEDLEAHFRNAHYCCTFQTCRVGKCYVFPYHTELLEH 300 (493)
T ss_pred hhhhccceecChHHHHHHHHhhhh-hhhhhhccCccchhhhhCHHHHHHHhhcCceEEEEEEEecCcEEEeccHHHHHHH
Confidence 599999999999999999986432 2333332221 222 2233344566654 4 2 367778888888
Q ss_pred Hhhcc
Q 041414 95 MRRHR 99 (152)
Q Consensus 95 ~~~h~ 99 (152)
+..-+
T Consensus 301 ~~~~h 305 (493)
T COG5236 301 LTRFH 305 (493)
T ss_pred HHHHh
Confidence 76533
No 115
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=49.35 E-value=11 Score=24.03 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=22.0
Q ss_pred CCceeccccccccccchHHHHHHhh
Q 041414 73 PKTHECSVCGLEFAIGQALGGHMRR 97 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~~H~~~ 97 (152)
.-.|-|-.|.+-|.....|..|.++
T Consensus 55 ~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 55 GGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CceeehhhhhhhhcchHHHHHHHhc
Confidence 4469999999999999999999864
No 116
>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=48.71 E-value=6.4 Score=23.75 Aligned_cols=14 Identities=43% Similarity=0.897 Sum_probs=11.7
Q ss_pred ceeccccccccccc
Q 041414 75 THECSVCGLEFAIG 88 (152)
Q Consensus 75 ~~~C~~C~k~F~~~ 88 (152)
.|.|..|++.|.-.
T Consensus 53 IW~C~~C~~~~AGG 66 (91)
T TIGR00280 53 IWTCRKCGAKFAGG 66 (91)
T ss_pred EEEcCCCCCEEeCC
Confidence 69999999998743
No 117
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=48.60 E-value=9.2 Score=23.02 Aligned_cols=14 Identities=36% Similarity=0.831 Sum_probs=8.1
Q ss_pred cceecCcccccCCC
Q 041414 27 RAFECKTCNRQFPS 40 (152)
Q Consensus 27 ~~~~C~~C~k~f~~ 40 (152)
+|-.|..||..|..
T Consensus 57 ~Pa~CkkCGfef~~ 70 (97)
T COG3357 57 RPARCKKCGFEFRD 70 (97)
T ss_pred cChhhcccCccccc
Confidence 35566666666643
No 118
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=48.37 E-value=11 Score=29.74 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=19.2
Q ss_pred eeccccccccccchHHHHHHh
Q 041414 76 HECSVCGLEFAIGQALGGHMR 96 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~~ 96 (152)
+-|.+|+++|.+..+|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 889999999999999999864
No 119
>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=47.78 E-value=7.2 Score=19.78 Aligned_cols=15 Identities=27% Similarity=0.758 Sum_probs=9.9
Q ss_pred Cceeccccccccccc
Q 041414 74 KTHECSVCGLEFAIG 88 (152)
Q Consensus 74 k~~~C~~C~k~F~~~ 88 (152)
-|+.|..|++.|=..
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 489999999999753
No 120
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=47.57 E-value=8.5 Score=24.87 Aligned_cols=15 Identities=40% Similarity=0.957 Sum_probs=12.2
Q ss_pred ceeccccccccccch
Q 041414 75 THECSVCGLEFAIGQ 89 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~ 89 (152)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 678999999998655
No 121
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=47.55 E-value=9.4 Score=20.20 Aligned_cols=18 Identities=39% Similarity=0.732 Sum_probs=14.4
Q ss_pred CCceeccccccccccchH
Q 041414 73 PKTHECSVCGLEFAIGQA 90 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~ 90 (152)
.+++.|..||..|.....
T Consensus 2 Dk~l~C~dCg~~FvfTa~ 19 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAG 19 (49)
T ss_pred CeeEEcccCCCeEEEehh
Confidence 467899999999886544
No 122
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=46.66 E-value=13 Score=18.06 Aligned_cols=11 Identities=27% Similarity=0.902 Sum_probs=5.5
Q ss_pred ceecCcccccC
Q 041414 28 AFECKTCNRQF 38 (152)
Q Consensus 28 ~~~C~~C~k~f 38 (152)
...|+.|+..|
T Consensus 25 ~v~C~~C~~~f 35 (36)
T PF13717_consen 25 KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEe
Confidence 44555555444
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=46.25 E-value=10 Score=19.07 Aligned_cols=12 Identities=17% Similarity=0.689 Sum_probs=10.3
Q ss_pred cceecCcccccC
Q 041414 27 RAFECKTCNRQF 38 (152)
Q Consensus 27 ~~~~C~~C~k~f 38 (152)
++-.|+.|+..|
T Consensus 28 ~~~~CpYCg~~y 39 (40)
T PF10276_consen 28 GPVVCPYCGTRY 39 (40)
T ss_dssp CEEEETTTTEEE
T ss_pred CeEECCCCCCEE
Confidence 578999999876
No 124
>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=45.40 E-value=8.2 Score=20.58 Aligned_cols=12 Identities=25% Similarity=0.675 Sum_probs=6.8
Q ss_pred eccccccccccc
Q 041414 77 ECSVCGLEFAIG 88 (152)
Q Consensus 77 ~C~~C~k~F~~~ 88 (152)
.|++|++.|...
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 899999999864
No 125
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.51 E-value=16 Score=23.61 Aligned_cols=16 Identities=25% Similarity=0.742 Sum_probs=12.8
Q ss_pred CCceeccccccccccc
Q 041414 73 PKTHECSVCGLEFAIG 88 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~ 88 (152)
...|.|+.|++.|...
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4569999999999753
No 126
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=44.25 E-value=2.9 Score=21.15 Aligned_cols=21 Identities=19% Similarity=0.194 Sum_probs=10.4
Q ss_pred chhcccCCCCCCCcccccccc
Q 041414 3 NCLMFMPHGGDFDAVNGVNMA 23 (152)
Q Consensus 3 ~C~~~~~~~~~~~~~~h~~~h 23 (152)
.|||.+.....-+...|.+.|
T Consensus 18 ~CgM~Y~~~~~eD~~~H~~yH 38 (41)
T PF13878_consen 18 TCGMLYSPGSPEDEKLHKKYH 38 (41)
T ss_pred CCCCEECCCCHHHHHHHHHHH
Confidence 466666555444433444433
No 127
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=42.34 E-value=8.9 Score=32.18 Aligned_cols=48 Identities=21% Similarity=0.352 Sum_probs=23.9
Q ss_pred ecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccc
Q 041414 30 ECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLE 84 (152)
Q Consensus 30 ~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~ 84 (152)
.|..||..+....- ..-+..|.......|..|+. ....|..|+.||-.
T Consensus 437 ~C~~Cg~v~~Cp~C-d~~lt~H~~~~~L~CH~Cg~------~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 437 LCRDCGYIAECPNC-DSPLTLHKATGQLRCHYCGY------QEPIPQSCPECGSE 484 (730)
T ss_pred ecccCCCcccCCCC-CcceEEecCCCeeEeCCCCC------CCCCCCCCCCCCCC
Confidence 46666655543210 11122333334445555543 23568889888854
No 128
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=42.21 E-value=8.7 Score=23.14 Aligned_cols=14 Identities=50% Similarity=0.985 Sum_probs=11.6
Q ss_pred ceeccccccccccc
Q 041414 75 THECSVCGLEFAIG 88 (152)
Q Consensus 75 ~~~C~~C~k~F~~~ 88 (152)
.|.|..|++.|.-.
T Consensus 54 IW~C~~C~~~~AGG 67 (90)
T PRK03976 54 IWECRKCGAKFAGG 67 (90)
T ss_pred EEEcCCCCCEEeCC
Confidence 69999999998743
No 129
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=41.85 E-value=18 Score=29.39 Aligned_cols=28 Identities=25% Similarity=0.500 Sum_probs=23.1
Q ss_pred CCcceecCcccccCCChhHHHHHHHhcC
Q 041414 25 ADRAFECKTCNRQFPSFQALGGHRASHK 52 (152)
Q Consensus 25 ~e~~~~C~~C~k~f~~~~~L~~h~~~h~ 52 (152)
...|..|..||..|........||..|.
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~ 442 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHD 442 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhh
Confidence 3567899999999999888887777664
No 130
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=41.20 E-value=15 Score=23.09 Aligned_cols=15 Identities=13% Similarity=0.226 Sum_probs=9.8
Q ss_pred CcceecCcccccCCC
Q 041414 26 DRAFECKTCNRQFPS 40 (152)
Q Consensus 26 e~~~~C~~C~k~f~~ 40 (152)
.-...|..||..|..
T Consensus 68 p~~~~C~~Cg~~~~~ 82 (113)
T PRK12380 68 PAQAWCWDCSQVVEI 82 (113)
T ss_pred CcEEEcccCCCEEec
Confidence 345678888876643
No 131
>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=40.83 E-value=9 Score=17.70 Aligned_cols=19 Identities=21% Similarity=0.497 Sum_probs=11.6
Q ss_pred eeccccccccccchHHHHHH
Q 041414 76 HECSVCGLEFAIGQALGGHM 95 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~L~~H~ 95 (152)
|.|-.|++.|.. ...+.|.
T Consensus 1 ~sCiDC~~~F~~-~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDFDG-DSYKSHT 19 (28)
T ss_dssp EEETTTTEEEEG-GGTTT--
T ss_pred CeeecCCCCcCc-CCcCCCC
Confidence 578889999953 3344454
No 132
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=39.78 E-value=24 Score=17.46 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=8.4
Q ss_pred ceecccccccc
Q 041414 75 THECSVCGLEF 85 (152)
Q Consensus 75 ~~~C~~C~k~F 85 (152)
-|.|..||..|
T Consensus 28 fy~C~~C~~~w 38 (39)
T PF01096_consen 28 FYVCCNCGHRW 38 (39)
T ss_dssp EEEESSSTEEE
T ss_pred EEEeCCCCCee
Confidence 38888888765
No 133
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=39.58 E-value=20 Score=22.87 Aligned_cols=24 Identities=33% Similarity=0.539 Sum_probs=21.2
Q ss_pred cceecCcccccCCChhHHHHHHHh
Q 041414 27 RAFECKTCNRQFPSFQALGGHRAS 50 (152)
Q Consensus 27 ~~~~C~~C~k~f~~~~~L~~h~~~ 50 (152)
-.|-|-.|.+-|.....|..|.++
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhc
Confidence 458999999999999999999764
No 134
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=39.41 E-value=19 Score=29.22 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=24.0
Q ss_pred CCceeccccccccccchHHHHHHhhccCC
Q 041414 73 PKTHECSVCGLEFAIGQALGGHMRRHRAG 101 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~~H~~~h~~~ 101 (152)
..|-.|..||..|........||..|...
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 46789999999999998888888777543
No 135
>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=38.94 E-value=16 Score=20.33 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=5.1
Q ss_pred ceecCcccccCC
Q 041414 28 AFECKTCNRQFP 39 (152)
Q Consensus 28 ~~~C~~C~k~f~ 39 (152)
.-.|..|++.|.
T Consensus 9 ~~~C~~C~~~F~ 20 (69)
T PF01363_consen 9 ASNCMICGKKFS 20 (69)
T ss_dssp -SB-TTT--B-B
T ss_pred CCcCcCcCCcCC
Confidence 346888888884
No 136
>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=38.75 E-value=18 Score=22.79 Aligned_cols=19 Identities=16% Similarity=0.489 Sum_probs=12.1
Q ss_pred ccCCCcceecCcccccCCC
Q 041414 22 MAVADRAFECKTCNRQFPS 40 (152)
Q Consensus 22 ~h~~e~~~~C~~C~k~f~~ 40 (152)
+..-.-...|..|+..|..
T Consensus 64 I~~~p~~~~C~~Cg~~~~~ 82 (115)
T TIGR00100 64 IEDEPVECECEDCSEEVSP 82 (115)
T ss_pred EEeeCcEEEcccCCCEEec
Confidence 3334445788888877654
No 137
>PRK14873 primosome assembly protein PriA; Provisional
Probab=38.40 E-value=26 Score=29.22 Aligned_cols=47 Identities=15% Similarity=0.277 Sum_probs=25.8
Q ss_pred ecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccc
Q 041414 30 ECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLE 84 (152)
Q Consensus 30 ~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~ 84 (152)
.|..||..+.... -...+..|.......|..|+.. ..|+.|+.||..
T Consensus 385 ~C~~Cg~~~~C~~-C~~~L~~h~~~~~l~Ch~CG~~-------~~p~~Cp~Cgs~ 431 (665)
T PRK14873 385 ACARCRTPARCRH-CTGPLGLPSAGGTPRCRWCGRA-------APDWRCPRCGSD 431 (665)
T ss_pred EhhhCcCeeECCC-CCCceeEecCCCeeECCCCcCC-------CcCccCCCCcCC
Confidence 5666665554321 1112233444455667777642 248899999854
No 138
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=38.19 E-value=70 Score=24.27 Aligned_cols=69 Identities=14% Similarity=0.119 Sum_probs=41.9
Q ss_pred cceecCcccccCCChhHHHHHHHhcCCCCCCC------------CCCCCcccccccCCCCceeccccccccccchHHHHH
Q 041414 27 RAFECKTCNRQFPSFQALGGHRASHKKSRVTE------------GSGGGVDTQQSPVKPKTHECSVCGLEFAIGQALGGH 94 (152)
Q Consensus 27 ~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~------------c~~~~~~h~~~h~~~k~~~C~~C~k~F~~~~~L~~H 94 (152)
-|-+|++|+-.+....+|.+--+.--.-++|. |..|... -.+.-.|.|..|...|-...+.-.|
T Consensus 289 LP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~----~~~~~~y~C~~Ck~~FCldCDv~iH 364 (378)
T KOG2807|consen 289 LPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGE----LLSSGRYRCESCKNVFCLDCDVFIH 364 (378)
T ss_pred CCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccc----cCCCCcEEchhccceeeccchHHHH
Confidence 46788999999888888875332111112221 2222110 0123359999999999888777777
Q ss_pred Hhhcc
Q 041414 95 MRRHR 99 (152)
Q Consensus 95 ~~~h~ 99 (152)
-..|.
T Consensus 365 esLh~ 369 (378)
T KOG2807|consen 365 ESLHN 369 (378)
T ss_pred hhhhc
Confidence 76664
No 139
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=37.96 E-value=30 Score=26.35 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=24.0
Q ss_pred ceeccccccccccchHHHHHHhh--ccCCCc
Q 041414 75 THECSVCGLEFAIGQALGGHMRR--HRAGAS 103 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~--h~~~~~ 103 (152)
.+.|-.|.+.|..+..|+.||+. |..-.|
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 58999999999999999999974 544444
No 140
>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=37.78 E-value=23 Score=28.10 Aligned_cols=28 Identities=29% Similarity=0.493 Sum_probs=24.0
Q ss_pred ceeccccccccccchHHHHHHh-hccCCC
Q 041414 75 THECSVCGLEFAIGQALGGHMR-RHRAGA 102 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~-~h~~~~ 102 (152)
-+.|+.|.+.|.....+..|+. .|.+.-
T Consensus 57 FWiCp~CskkF~d~~~~~~H~~~eH~~~l 85 (466)
T PF04780_consen 57 FWICPRCSKKFSDAESCLSHMEQEHPAGL 85 (466)
T ss_pred EeeCCcccceeCCHHHHHHHHHHhhhhhc
Confidence 5789999999999999999997 476653
No 141
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=37.65 E-value=27 Score=19.40 Aligned_cols=15 Identities=27% Similarity=0.738 Sum_probs=11.5
Q ss_pred CCceecccccccccc
Q 041414 73 PKTHECSVCGLEFAI 87 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~ 87 (152)
.+.|.|+.||..+..
T Consensus 44 ~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 44 GRVFTCPNCGFEMDR 58 (69)
T ss_pred cceEEcCCCCCEECc
Confidence 567999999977654
No 142
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.74 E-value=21 Score=22.59 Aligned_cols=19 Identities=26% Similarity=0.646 Sum_probs=12.3
Q ss_pred ccCCCcceecCcccccCCC
Q 041414 22 MAVADRAFECKTCNRQFPS 40 (152)
Q Consensus 22 ~h~~e~~~~C~~C~k~f~~ 40 (152)
+..-.-.+.|..||..|..
T Consensus 65 Ie~vp~~~~C~~Cg~~~~~ 83 (117)
T PRK00564 65 IVDEKVELECKDCSHVFKP 83 (117)
T ss_pred EEecCCEEEhhhCCCcccc
Confidence 3334455788888877654
No 143
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=35.95 E-value=20 Score=22.16 Aligned_cols=16 Identities=38% Similarity=0.872 Sum_probs=12.7
Q ss_pred ceeccccccccccchH
Q 041414 75 THECSVCGLEFAIGQA 90 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~ 90 (152)
|+.|..||..|...+.
T Consensus 2 pH~CtrCG~vf~~g~~ 17 (112)
T COG3364 2 PHQCTRCGEVFDDGSE 17 (112)
T ss_pred CceecccccccccccH
Confidence 6789999999987543
No 144
>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=35.62 E-value=16 Score=18.66 Aligned_cols=15 Identities=33% Similarity=0.767 Sum_probs=11.5
Q ss_pred eeccccccccccchH
Q 041414 76 HECSVCGLEFAIGQA 90 (152)
Q Consensus 76 ~~C~~C~k~F~~~~~ 90 (152)
-.|..||+.|.....
T Consensus 9 K~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 9 KICPVCGRPFTWRKK 23 (42)
T ss_pred CcCcccCCcchHHHH
Confidence 359999999986543
No 145
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=35.38 E-value=26 Score=27.61 Aligned_cols=29 Identities=17% Similarity=0.367 Sum_probs=24.4
Q ss_pred cccCCCCceeccccc-cccccchHHHHHHh
Q 041414 68 QSPVKPKTHECSVCG-LEFAIGQALGGHMR 96 (152)
Q Consensus 68 ~~h~~~k~~~C~~C~-k~F~~~~~L~~H~~ 96 (152)
+.|.-.+.|.|.+|| .++.-...+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 556777889999999 88888889999964
No 146
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=35.36 E-value=45 Score=24.21 Aligned_cols=59 Identities=17% Similarity=0.296 Sum_probs=29.9
Q ss_pred ccCCCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccc----cCCCCceeccccccccccc
Q 041414 22 MAVADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQS----PVKPKTHECSVCGLEFAIG 88 (152)
Q Consensus 22 ~h~~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~----h~~~k~~~C~~C~k~F~~~ 88 (152)
|-+..+.|.|..|...+= .++-.....-+|..|....--+ =-|---|.|+.|+..|...
T Consensus 106 ip~~drqFaC~~Cd~~Ww--------Rrvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 106 IPSVDRQFACSSCDHMWW--------RRVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred ccccceeeeccccchHHH--------hccCcccccccccccccccCCCccccccceeeeecccccccchhh
Confidence 344557788888864321 1222222233455554411100 0122348888888888754
No 147
>COG1773 Rubredoxin [Energy production and conversion]
Probab=35.23 E-value=18 Score=19.66 Aligned_cols=15 Identities=40% Similarity=0.829 Sum_probs=11.6
Q ss_pred Cceeccccccccccc
Q 041414 74 KTHECSVCGLEFAIG 88 (152)
Q Consensus 74 k~~~C~~C~k~F~~~ 88 (152)
+.|+|..||..|.-.
T Consensus 2 ~~~~C~~CG~vYd~e 16 (55)
T COG1773 2 KRWRCSVCGYVYDPE 16 (55)
T ss_pred CceEecCCceEeccc
Confidence 358999999888653
No 148
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=34.15 E-value=41 Score=17.17 Aligned_cols=11 Identities=18% Similarity=0.489 Sum_probs=7.2
Q ss_pred CCceecccccc
Q 041414 73 PKTHECSVCGL 83 (152)
Q Consensus 73 ~k~~~C~~C~k 83 (152)
...|+|..|++
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 45677777764
No 149
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=33.53 E-value=22 Score=27.96 Aligned_cols=28 Identities=25% Similarity=0.438 Sum_probs=24.3
Q ss_pred CceeccccccccccchHHHHHHhh-ccCC
Q 041414 74 KTHECSVCGLEFAIGQALGGHMRR-HRAG 101 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L~~H~~~-h~~~ 101 (152)
..|.|++|.+-|.....|..|... |.++
T Consensus 14 egflCPiC~~dl~~~~~L~~H~d~eH~~e 42 (505)
T KOG1842|consen 14 EGFLCPICLLDLPNLSALNDHLDVEHFEE 42 (505)
T ss_pred hcccCchHhhhhhhHHHHHHHHhhhcccc
Confidence 469999999999999999999975 5554
No 150
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=33.49 E-value=24 Score=22.19 Aligned_cols=16 Identities=19% Similarity=0.466 Sum_probs=10.1
Q ss_pred CCCcceecCcccccCC
Q 041414 24 VADRAFECKTCNRQFP 39 (152)
Q Consensus 24 ~~e~~~~C~~C~k~f~ 39 (152)
.-.-...|..||..|.
T Consensus 66 ~~p~~~~C~~Cg~~~~ 81 (114)
T PRK03681 66 EQEAECWCETCQQYVT 81 (114)
T ss_pred eeCcEEEcccCCCeee
Confidence 3344577888887654
No 151
>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=33.22 E-value=29 Score=18.35 Aligned_cols=11 Identities=27% Similarity=0.866 Sum_probs=7.2
Q ss_pred ecCcccccCCC
Q 041414 30 ECKTCNRQFPS 40 (152)
Q Consensus 30 ~C~~C~k~f~~ 40 (152)
.|..|++.|..
T Consensus 4 ~C~~C~~~F~~ 14 (57)
T cd00065 4 SCMGCGKPFTL 14 (57)
T ss_pred cCcccCccccC
Confidence 46677777753
No 152
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=33.13 E-value=30 Score=27.09 Aligned_cols=21 Identities=19% Similarity=0.649 Sum_probs=15.2
Q ss_pred cCCCcceecCcccccCCChhH
Q 041414 23 AVADRAFECKTCNRQFPSFQA 43 (152)
Q Consensus 23 h~~e~~~~C~~C~k~f~~~~~ 43 (152)
-+...-|.|+.|.+.|..-..
T Consensus 123 ~t~~~~Y~Cp~C~kkyt~Lea 143 (436)
T KOG2593|consen 123 DTNVAGYVCPNCQKKYTSLEA 143 (436)
T ss_pred ccccccccCCccccchhhhHH
Confidence 345567999999999965443
No 153
>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=32.87 E-value=20 Score=23.44 Aligned_cols=20 Identities=25% Similarity=0.486 Sum_probs=15.1
Q ss_pred cccCCCCceeccccccccccc
Q 041414 68 QSPVKPKTHECSVCGLEFAIG 88 (152)
Q Consensus 68 ~~h~~~k~~~C~~C~k~F~~~ 88 (152)
..+.+ ++..|++||..|.-.
T Consensus 106 ~l~~g-~~~RCpeCG~~fkL~ 125 (136)
T PF01215_consen 106 WLHKG-KPQRCPECGQVFKLK 125 (136)
T ss_dssp EEETT-SEEEETTTEEEEEEE
T ss_pred EEeCC-CccCCCCCCeEEEEE
Confidence 34555 589999999999753
No 154
>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=32.74 E-value=13 Score=29.72 Aligned_cols=47 Identities=21% Similarity=0.352 Sum_probs=22.4
Q ss_pred ecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceecccccc
Q 041414 30 ECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGL 83 (152)
Q Consensus 30 ~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k 83 (152)
.|..||....... -...+..|.......|..|+.. ...|..|+.||.
T Consensus 215 ~C~~Cg~~~~C~~-C~~~l~~h~~~~~l~Ch~Cg~~------~~~~~~Cp~C~s 261 (505)
T TIGR00595 215 LCRSCGYILCCPN-CDVSLTYHKKEGKLRCHYCGYQ------EPIPKTCPQCGS 261 (505)
T ss_pred EhhhCcCccCCCC-CCCceEEecCCCeEEcCCCcCc------CCCCCCCCCCCC
Confidence 4555555544321 1112233334444455555432 245778888875
No 155
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=32.40 E-value=50 Score=16.42 Aligned_cols=12 Identities=25% Similarity=0.683 Sum_probs=8.8
Q ss_pred ceeccccccccc
Q 041414 75 THECSVCGLEFA 86 (152)
Q Consensus 75 ~~~C~~C~k~F~ 86 (152)
-|.|..||..|.
T Consensus 28 fy~C~~C~~~w~ 39 (40)
T smart00440 28 FYVCTKCGHRWR 39 (40)
T ss_pred EEEeCCCCCEeC
Confidence 488888887654
No 156
>PHA02998 RNA polymerase subunit; Provisional
Probab=31.39 E-value=39 Score=23.17 Aligned_cols=12 Identities=33% Similarity=0.753 Sum_probs=8.9
Q ss_pred eecccccccccc
Q 041414 76 HECSVCGLEFAI 87 (152)
Q Consensus 76 ~~C~~C~k~F~~ 87 (152)
|.|..||..|..
T Consensus 172 YkC~~CG~~wkp 183 (195)
T PHA02998 172 HACRDCKKHFKP 183 (195)
T ss_pred EEcCCCCCccCC
Confidence 778888877654
No 157
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=31.05 E-value=32 Score=17.25 Aligned_cols=11 Identities=36% Similarity=0.848 Sum_probs=6.5
Q ss_pred ceecccccccc
Q 041414 75 THECSVCGLEF 85 (152)
Q Consensus 75 ~~~C~~C~k~F 85 (152)
-+.|..||...
T Consensus 19 ~~vC~~CG~Vl 29 (43)
T PF08271_consen 19 ELVCPNCGLVL 29 (43)
T ss_dssp EEEETTT-BBE
T ss_pred eEECCCCCCEe
Confidence 46777777554
No 158
>PTZ00448 hypothetical protein; Provisional
Probab=31.02 E-value=32 Score=26.44 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=21.7
Q ss_pred ceeccccccccccchHHHHHHhhcc
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHR 99 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~ 99 (152)
.|.|..|+-.|......+.|+++-.
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KSDw 338 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRSEW 338 (373)
T ss_pred CccccccccccCCHHHHHHHhhhhH
Confidence 5889999999998888899998743
No 159
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=30.77 E-value=32 Score=26.16 Aligned_cols=23 Identities=22% Similarity=0.479 Sum_probs=21.0
Q ss_pred ceecCcccccCCChhHHHHHHHh
Q 041414 28 AFECKTCNRQFPSFQALGGHRAS 50 (152)
Q Consensus 28 ~~~C~~C~k~f~~~~~L~~h~~~ 50 (152)
.+.|-.|.+.|+.+..|+.||+.
T Consensus 195 r~~CLyCekifrdkntLkeHMrk 217 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRK 217 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHh
Confidence 47899999999999999999985
No 160
>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=30.12 E-value=17 Score=25.28 Aligned_cols=29 Identities=17% Similarity=0.373 Sum_probs=0.0
Q ss_pred cccCCCCceeccccc-cccccchHHHHHHh
Q 041414 68 QSPVKPKTHECSVCG-LEFAIGQALGGHMR 96 (152)
Q Consensus 68 ~~h~~~k~~~C~~C~-k~F~~~~~L~~H~~ 96 (152)
+.|--.+.|.|.+|| .+|.-...+.+|..
T Consensus 94 KLhGL~~ey~CEICGN~~Y~GrkaFekHF~ 123 (196)
T PF11931_consen 94 KLHGLGVEYKCEICGNQSYKGRKAFEKHFQ 123 (196)
T ss_dssp ------------------------------
T ss_pred HHhCCCCeeeeEeCCCcceecHHHHHHhcC
Confidence 445556789999999 46667777777753
No 161
>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=30.06 E-value=22 Score=19.23 Aligned_cols=31 Identities=19% Similarity=0.353 Sum_probs=18.1
Q ss_pred ceeccccccccccchHHHHHHhhccCCCcccccccccc
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHRAGASHANEKLSAF 112 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~~~~~~~~~~~~~~ 112 (152)
.|+|+.||..+.-... ..|+...++.|+..+
T Consensus 2 ~~~CP~CG~~iev~~~-------~~GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENP-------ELGELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCC-------ccCCEEeCCCCCCEE
Confidence 3789999987753322 124544456666443
No 162
>PF14353 CpXC: CpXC protein
Probab=29.21 E-value=25 Score=22.36 Aligned_cols=22 Identities=27% Similarity=0.484 Sum_probs=16.2
Q ss_pred CceeccccccccccchHHHHHH
Q 041414 74 KTHECSVCGLEFAIGQALGGHM 95 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L~~H~ 95 (152)
-.|.|+.||..|.-...+..|-
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred CEEECCCCCCceecCCCEEEEc
Confidence 3699999999998665554443
No 163
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=29.05 E-value=27 Score=24.88 Aligned_cols=15 Identities=20% Similarity=0.410 Sum_probs=13.0
Q ss_pred CCceecccccccccc
Q 041414 73 PKTHECSVCGLEFAI 87 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~ 87 (152)
.++.+|.+||..|.-
T Consensus 179 GkpqRCpECGqVFKL 193 (268)
T PTZ00043 179 GFLYRCGECDQIFML 193 (268)
T ss_pred CCCccCCCCCcEEEE
Confidence 468999999999985
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=28.94 E-value=28 Score=22.99 Aligned_cols=6 Identities=50% Similarity=1.542 Sum_probs=3.2
Q ss_pred eccccc
Q 041414 77 ECSVCG 82 (152)
Q Consensus 77 ~C~~C~ 82 (152)
.|+.||
T Consensus 132 ~Cp~C~ 137 (146)
T PF07295_consen 132 PCPKCG 137 (146)
T ss_pred CCCCCC
Confidence 455555
No 165
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.68 E-value=32 Score=26.95 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=12.3
Q ss_pred Cceeccccccccccch
Q 041414 74 KTHECSVCGLEFAIGQ 89 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~ 89 (152)
.-|+|+.||..+....
T Consensus 366 ~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 366 NGFRCKKCGTRARETL 381 (421)
T ss_pred CCcccccccccCCccc
Confidence 3799999998877643
No 166
>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=26.74 E-value=45 Score=26.39 Aligned_cols=11 Identities=18% Similarity=0.393 Sum_probs=7.5
Q ss_pred Cceeccccccc
Q 041414 74 KTHECSVCGLE 84 (152)
Q Consensus 74 k~~~C~~C~k~ 84 (152)
..++|+.|+.+
T Consensus 20 ~~g~Cp~C~~w 30 (454)
T TIGR00416 20 WQGKCPACHAW 30 (454)
T ss_pred ccEECcCCCCc
Confidence 45788888743
No 167
>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=26.54 E-value=74 Score=15.24 Aligned_cols=24 Identities=25% Similarity=0.499 Sum_probs=15.5
Q ss_pred ceeccccccccccchHHHHHHhhcc
Q 041414 75 THECSVCGLEFAIGQALGGHMRRHR 99 (152)
Q Consensus 75 ~~~C~~C~k~F~~~~~L~~H~~~h~ 99 (152)
.+.|+.|++.+.. +-+..|+..-.
T Consensus 4 ~~~C~nC~R~v~a-~RfA~HLekCm 27 (33)
T PF08209_consen 4 YVECPNCGRPVAA-SRFAPHLEKCM 27 (33)
T ss_dssp EEE-TTTSSEEEG-GGHHHHHHHHT
T ss_pred eEECCCCcCCcch-hhhHHHHHHHH
Confidence 5789999998764 34566765433
No 168
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=26.08 E-value=31 Score=18.90 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=16.2
Q ss_pred cchhcccCCCCCCCccccccccCCCcceecCcccccC
Q 041414 2 ANCLMFMPHGGDFDAVNGVNMAVADRAFECKTCNRQF 38 (152)
Q Consensus 2 ~~C~~~~~~~~~~~~~~h~~~h~~e~~~~C~~C~k~f 38 (152)
|+||+.|...++-. +--.|+.|.+-|
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 78998887665533 123577776544
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=26.03 E-value=18 Score=19.29 Aligned_cols=26 Identities=23% Similarity=0.322 Sum_probs=13.3
Q ss_pred CceeccccccccccchHHHHHHhhcc
Q 041414 74 KTHECSVCGLEFAIGQALGGHMRRHR 99 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L~~H~~~h~ 99 (152)
..|+|+.|...|=..-.+-.|...|.
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 46888888888876666655655553
No 170
>PRK11823 DNA repair protein RadA; Provisional
Probab=26.01 E-value=48 Score=26.18 Aligned_cols=12 Identities=25% Similarity=0.791 Sum_probs=8.2
Q ss_pred cceecCcccccC
Q 041414 27 RAFECKTCNRQF 38 (152)
Q Consensus 27 ~~~~C~~C~k~f 38 (152)
..|.|..||..+
T Consensus 6 ~~y~C~~Cg~~~ 17 (446)
T PRK11823 6 TAYVCQECGAES 17 (446)
T ss_pred CeEECCcCCCCC
Confidence 357888887654
No 171
>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 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=25.71 E-value=32 Score=16.33 Aligned_cols=11 Identities=36% Similarity=0.779 Sum_probs=7.6
Q ss_pred eeccccccccc
Q 041414 76 HECSVCGLEFA 86 (152)
Q Consensus 76 ~~C~~C~k~F~ 86 (152)
|.|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 56888887766
No 173
>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=25.26 E-value=33 Score=16.82 Aligned_cols=12 Identities=17% Similarity=0.755 Sum_probs=6.3
Q ss_pred cceecCcccccC
Q 041414 27 RAFECKTCNRQF 38 (152)
Q Consensus 27 ~~~~C~~C~k~f 38 (152)
+-|+|..||...
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 458899888653
No 174
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=25.07 E-value=44 Score=24.87 Aligned_cols=59 Identities=19% Similarity=0.270 Sum_probs=31.4
Q ss_pred CcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCcccccccCCCCceeccccccc----cccchHHHHHHhh
Q 041414 26 DRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGVDTQQSPVKPKTHECSVCGLE----FAIGQALGGHMRR 97 (152)
Q Consensus 26 e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~~h~~~h~~~k~~~C~~C~k~----F~~~~~L~~H~~~ 97 (152)
.-||.|.+|.+.|...- -+.-..+-|..|...+. .+.-+|.+|++. |.....|..-+..
T Consensus 239 ~~Pf~c~icr~~f~~pV--------vt~c~h~fc~~ca~~~~-----qk~~~c~vC~~~t~g~~~~akeL~~~L~~ 301 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRPV--------VTKCGHYFCEVCALKPY-----QKGEKCYVCSQQTHGSFNVAKELLVSLKL 301 (313)
T ss_pred cCCccccccccccccch--------hhcCCceeehhhhcccc-----ccCCcceecccccccccchHHHHHHHHHh
Confidence 45899999999987542 12222333444433222 233467777753 4444455544443
No 175
>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=25.06 E-value=30 Score=23.09 Aligned_cols=20 Identities=10% Similarity=0.160 Sum_probs=9.0
Q ss_pred chhcccCCCCCCCccccccc
Q 041414 3 NCLMFMPHGGDFDAVNGVNM 22 (152)
Q Consensus 3 ~C~~~~~~~~~~~~~~h~~~ 22 (152)
.|+|.|.+++.-....|+..
T Consensus 19 ~c~kWFCNg~~~~s~SHIv~ 38 (152)
T PF09416_consen 19 TCNKWFCNGRGNTSGSHIVN 38 (152)
T ss_dssp TTTEEEES--TTSSS-HHHH
T ss_pred CCCcEeecCCCCCcccHHHH
Confidence 35667766655443445433
No 176
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=24.82 E-value=31 Score=18.27 Aligned_cols=13 Identities=31% Similarity=0.649 Sum_probs=10.9
Q ss_pred CCceecccccccc
Q 041414 73 PKTHECSVCGLEF 85 (152)
Q Consensus 73 ~k~~~C~~C~k~F 85 (152)
...|.|..||+.|
T Consensus 4 ~~~Y~C~~Cg~~~ 16 (49)
T COG1996 4 MMEYKCARCGREV 16 (49)
T ss_pred eEEEEhhhcCCee
Confidence 3469999999998
No 177
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=24.78 E-value=48 Score=26.38 Aligned_cols=21 Identities=33% Similarity=0.678 Sum_probs=18.5
Q ss_pred eecCcccccCCChhHHHHHHH
Q 041414 29 FECKTCNRQFPSFQALGGHRA 49 (152)
Q Consensus 29 ~~C~~C~k~f~~~~~L~~h~~ 49 (152)
+-|.+|+|+|.+.-.|..|..
T Consensus 293 lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred eEEeeccccccchHHHHhhHH
Confidence 789999999999988888864
No 178
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=24.62 E-value=46 Score=25.47 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=22.7
Q ss_pred cccCCCCceeccccc-cccccchHHHHHHh
Q 041414 68 QSPVKPKTHECSVCG-LEFAIGQALGGHMR 96 (152)
Q Consensus 68 ~~h~~~k~~~C~~C~-k~F~~~~~L~~H~~ 96 (152)
+.|.-.+-|.|.+|| +++.....+.+|..
T Consensus 367 klhgLd~ef~CEICgNyvy~GR~~FdrHF~ 396 (470)
T COG5188 367 KLHGLDIEFECEICGNYVYYGRDRFDRHFE 396 (470)
T ss_pred HhcCCCcceeeeecccccccchHHHHhhhh
Confidence 346667889999999 78877777888863
No 179
>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=24.45 E-value=32 Score=16.66 Aligned_cols=13 Identities=31% Similarity=0.718 Sum_probs=6.6
Q ss_pred eccccccccccch
Q 041414 77 ECSVCGLEFAIGQ 89 (152)
Q Consensus 77 ~C~~C~k~F~~~~ 89 (152)
.|.+|++.|..+.
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 6888998887543
No 180
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=23.85 E-value=19 Score=30.15 Aligned_cols=51 Identities=16% Similarity=0.255 Sum_probs=28.6
Q ss_pred ecCcccccCCChhHHHHHHHhcCCCCCCC-CCCCCc-----ccccccCCCCceecccccc
Q 041414 30 ECKTCNRQFPSFQALGGHRASHKKSRVTE-GSGGGV-----DTQQSPVKPKTHECSVCGL 83 (152)
Q Consensus 30 ~C~~C~k~f~~~~~L~~h~~~h~~~~~~~-c~~~~~-----~h~~~h~~~k~~~C~~C~k 83 (152)
.|..||-.|+-...|... |-++.=+.|. |+.|.+ ...+-|. .|..|+.||-
T Consensus 125 ~CT~CGPRfTIi~alPYD-R~nTsM~~F~lC~~C~~EY~dP~nRRfHA--Qp~aCp~CGP 181 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD-RENTSMADFPLCPFCDKEYKDPLNRRFHA--QPIACPKCGP 181 (750)
T ss_pred ccCCCCcceeeeccCCCC-cccCccccCcCCHHHHHHhcCcccccccc--ccccCcccCC
Confidence 478888888766555433 2233333343 666654 2223343 3678999985
No 181
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.55 E-value=74 Score=26.63 Aligned_cols=72 Identities=18% Similarity=0.215 Sum_probs=36.6
Q ss_pred ecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc-----------ccccccCCCCceecc--ccc-cccccc----hHH
Q 041414 30 ECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV-----------DTQQSPVKPKTHECS--VCG-LEFAIG----QAL 91 (152)
Q Consensus 30 ~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~-----------~h~~~h~~~k~~~C~--~C~-k~F~~~----~~L 91 (152)
.|..|...|.....|.+|++.++- .|..|.+ .-+..|-.+..|.|. .|. +.|... ..|
T Consensus 184 ~C~~C~~~fld~~el~rH~~~~h~----~chfC~~~~~~neyy~~~~dLe~HfR~~HflCE~~~C~~~~f~~~~~~ei~l 259 (669)
T KOG2231|consen 184 LCKFCHERFLDDDELYRHLRFDHE----FCHFCDYKTGQNEYYNDYDDLEEHFRKGHFLCEEEFCRTKKFYVAFELEIEL 259 (669)
T ss_pred cchhhhhhhccHHHHHHhhcccee----heeecCcccccchhcccchHHHHHhhhcCccccccccccceeeehhHHHHHH
Confidence 466777777777777777664332 2222210 223445556678887 454 334433 444
Q ss_pred HHHHhhccCCCccc
Q 041414 92 GGHMRRHRAGASHA 105 (152)
Q Consensus 92 ~~H~~~h~~~~~~~ 105 (152)
++|.+.+..++.|.
T Consensus 260 k~~~~~~~~e~~~~ 273 (669)
T KOG2231|consen 260 KAHNRFIQHEKCYI 273 (669)
T ss_pred Hhhccccchheecc
Confidence 44443333343333
No 182
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.43 E-value=86 Score=16.08 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=8.7
Q ss_pred ceeccccccccc
Q 041414 75 THECSVCGLEFA 86 (152)
Q Consensus 75 ~~~C~~C~k~F~ 86 (152)
.|.|+.||..+.
T Consensus 20 ~~vC~~Cg~~~~ 31 (52)
T smart00661 20 RFVCRKCGYEEP 31 (52)
T ss_pred EEECCcCCCeEE
Confidence 578888886544
No 183
>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=22.95 E-value=36 Score=16.58 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=8.6
Q ss_pred eecccccccccc
Q 041414 76 HECSVCGLEFAI 87 (152)
Q Consensus 76 ~~C~~C~k~F~~ 87 (152)
+.|+.||+.|.-
T Consensus 2 r~C~~Cg~~Yh~ 13 (36)
T PF05191_consen 2 RICPKCGRIYHI 13 (36)
T ss_dssp EEETTTTEEEET
T ss_pred cCcCCCCCcccc
Confidence 468888888763
No 184
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=22.27 E-value=43 Score=20.85 Aligned_cols=24 Identities=29% Similarity=0.425 Sum_probs=20.7
Q ss_pred CCceeccccccccccchHHHHHHh
Q 041414 73 PKTHECSVCGLEFAIGQALGGHMR 96 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~~H~~ 96 (152)
.-.|-|.+|.+-|-+...|..|.+
T Consensus 53 lGqhYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 53 LGQHYCIECARYFITEKALMEHKK 76 (126)
T ss_pred CceeeeehhHHHHHHHHHHHHHhc
Confidence 345889999999999999999976
No 185
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=22.17 E-value=48 Score=20.72 Aligned_cols=15 Identities=20% Similarity=0.403 Sum_probs=11.6
Q ss_pred Cceeccccccccccc
Q 041414 74 KTHECSVCGLEFAIG 88 (152)
Q Consensus 74 k~~~C~~C~k~F~~~ 88 (152)
..|.|++|+..+...
T Consensus 18 ~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 18 TQLICPSCLYEWNEN 32 (109)
T ss_pred CeeECcccccccccc
Confidence 369999999777654
No 186
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.87 E-value=56 Score=21.17 Aligned_cols=20 Identities=10% Similarity=0.539 Sum_probs=14.4
Q ss_pred ccCCCcceecCcccccCCCh
Q 041414 22 MAVADRAFECKTCNRQFPSF 41 (152)
Q Consensus 22 ~h~~e~~~~C~~C~k~f~~~ 41 (152)
+-.....+.|..||..|...
T Consensus 64 i~~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 64 FEEEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred EEecceEEECCCCCCEEecc
Confidence 33445678999999888654
No 187
>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=21.76 E-value=43 Score=17.48 Aligned_cols=13 Identities=31% Similarity=0.830 Sum_probs=9.8
Q ss_pred eeccccccccccc
Q 041414 76 HECSVCGLEFAIG 88 (152)
Q Consensus 76 ~~C~~C~k~F~~~ 88 (152)
|.|..||..+...
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 7888898777654
No 188
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=21.70 E-value=38 Score=16.61 Aligned_cols=14 Identities=29% Similarity=0.653 Sum_probs=8.6
Q ss_pred eccccccccccchH
Q 041414 77 ECSVCGLEFAIGQA 90 (152)
Q Consensus 77 ~C~~C~k~F~~~~~ 90 (152)
.|+.|++.|-..+.
T Consensus 4 ~CprC~kg~Hwa~~ 17 (36)
T PF14787_consen 4 LCPRCGKGFHWASE 17 (36)
T ss_dssp C-TTTSSSCS-TTT
T ss_pred cCcccCCCcchhhh
Confidence 57888888776554
No 189
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=21.41 E-value=47 Score=15.83 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=9.4
Q ss_pred ceeccccccccc
Q 041414 75 THECSVCGLEFA 86 (152)
Q Consensus 75 ~~~C~~C~k~F~ 86 (152)
-+.|..||.+|.
T Consensus 21 ~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 21 YEVCIFCGSSFP 32 (33)
T ss_pred eEEcccCCcEee
Confidence 467999998875
No 190
>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=21.32 E-value=38 Score=17.91 Aligned_cols=13 Identities=31% Similarity=0.869 Sum_probs=10.0
Q ss_pred eeccccccccccc
Q 041414 76 HECSVCGLEFAIG 88 (152)
Q Consensus 76 ~~C~~C~k~F~~~ 88 (152)
|.|..||..+...
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 7899999877643
No 191
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=21.30 E-value=43 Score=22.32 Aligned_cols=10 Identities=30% Similarity=0.776 Sum_probs=7.1
Q ss_pred ceeccccccc
Q 041414 75 THECSVCGLE 84 (152)
Q Consensus 75 ~~~C~~C~k~ 84 (152)
.|.|..|+-.
T Consensus 140 ~YrC~~C~gk 149 (156)
T COG3091 140 VYRCGKCGGK 149 (156)
T ss_pred eEEeccCCce
Confidence 6888887643
No 192
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=21.13 E-value=42 Score=24.28 Aligned_cols=31 Identities=13% Similarity=0.184 Sum_probs=11.6
Q ss_pred CCCCCCcccccccC---CCCceeccccccccccc
Q 041414 58 EGSGGGVDTQQSPV---KPKTHECSVCGLEFAIG 88 (152)
Q Consensus 58 ~c~~~~~~h~~~h~---~~k~~~C~~C~k~F~~~ 88 (152)
.|+.|+..++.... ....|-|+.|+..|--+
T Consensus 33 yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELK 66 (254)
T PF06044_consen 33 YCPNCGSKPLSKFENNRPVADFYCPNCNEEYELK 66 (254)
T ss_dssp --TTT--SS-EE--------EEE-TTT--EEEEE
T ss_pred cCCCCCChhHhhccCCCccceeECCCCchHHhhh
Confidence 36666654333322 23459999998887643
No 193
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=20.88 E-value=31 Score=28.90 Aligned_cols=22 Identities=18% Similarity=0.489 Sum_probs=16.1
Q ss_pred CCceeccccccccccchHHHHH
Q 041414 73 PKTHECSVCGLEFAIGQALGGH 94 (152)
Q Consensus 73 ~k~~~C~~C~k~F~~~~~L~~H 94 (152)
-+.-+||.|+.+|....-+..|
T Consensus 676 tRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 676 TRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred HhcCCCCCCCCCCCcccccccC
Confidence 3567899999999876654433
No 194
>PLN02748 tRNA dimethylallyltransferase
Probab=20.83 E-value=62 Score=25.83 Aligned_cols=24 Identities=17% Similarity=0.310 Sum_probs=20.7
Q ss_pred Cceecccccc-ccccchHHHHHHhh
Q 041414 74 KTHECSVCGL-EFAIGQALGGHMRR 97 (152)
Q Consensus 74 k~~~C~~C~k-~F~~~~~L~~H~~~ 97 (152)
+.|.|..|++ .+........|++.
T Consensus 417 ~~~~Ce~C~~~~~~G~~eW~~Hlks 441 (468)
T PLN02748 417 TQYVCEACGNKVLRGAHEWEQHKQG 441 (468)
T ss_pred ccccccCCCCcccCCHHHHHHHhcc
Confidence 6789999997 89999889999864
No 195
>PF14369 zf-RING_3: zinc-finger
Probab=20.73 E-value=65 Score=15.55 Aligned_cols=10 Identities=30% Similarity=0.886 Sum_probs=7.4
Q ss_pred ecCcccccCC
Q 041414 30 ECKTCNRQFP 39 (152)
Q Consensus 30 ~C~~C~k~f~ 39 (152)
.|+.|+..|.
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4888887774
No 196
>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=20.70 E-value=65 Score=24.82 Aligned_cols=11 Identities=27% Similarity=0.486 Sum_probs=7.4
Q ss_pred Cceeccccccc
Q 041414 74 KTHECSVCGLE 84 (152)
Q Consensus 74 k~~~C~~C~k~ 84 (152)
+..+|+.|+.+
T Consensus 13 ~~g~cp~c~~w 23 (372)
T cd01121 13 WLGKCPECGEW 23 (372)
T ss_pred ccEECcCCCCc
Confidence 45778888753
No 197
>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=20.66 E-value=47 Score=17.72 Aligned_cols=18 Identities=17% Similarity=0.346 Sum_probs=11.9
Q ss_pred CCCCceeccccccccccc
Q 041414 71 VKPKTHECSVCGLEFAIG 88 (152)
Q Consensus 71 ~~~k~~~C~~C~k~F~~~ 88 (152)
.....|+|.+|++.|...
T Consensus 31 ~~~~~~rC~YCe~~~~~~ 48 (52)
T PF02748_consen 31 KEPIKLRCHYCERIITED 48 (52)
T ss_dssp TTTCEEEETTT--EEEHH
T ss_pred CCCCEEEeeCCCCEeccc
Confidence 445679999999987643
No 198
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.43 E-value=51 Score=24.77 Aligned_cols=50 Identities=12% Similarity=0.086 Sum_probs=27.9
Q ss_pred CCcceecCcccccCCChhHHHHHHHhcCCCCCCCCCCCCc-ccccccCCCCceecccccc
Q 041414 25 ADRAFECKTCNRQFPSFQALGGHRASHKKSRVTEGSGGGV-DTQQSPVKPKTHECSVCGL 83 (152)
Q Consensus 25 ~e~~~~C~~C~k~f~~~~~L~~h~~~h~~~~~~~c~~~~~-~h~~~h~~~k~~~C~~C~k 83 (152)
++..-.|++||..=. .+ +. +.....|.+-..|..|.. .|. ..-+|+.||.
T Consensus 184 ~~~~~~CPvCGs~P~-~s-~v-~~~~~~G~RyL~CslC~teW~~------~R~~C~~Cg~ 234 (309)
T PRK03564 184 GEQRQFCPVCGSMPV-SS-VV-QIGTTQGLRYLHCNLCESEWHV------VRVKCSNCEQ 234 (309)
T ss_pred ccCCCCCCCCCCcch-hh-ee-eccCCCCceEEEcCCCCCcccc------cCccCCCCCC
Confidence 345568999996521 11 11 222345556566777765 221 2357888885
No 199
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=20.33 E-value=62 Score=22.08 Aligned_cols=21 Identities=24% Similarity=0.407 Sum_probs=16.3
Q ss_pred CceeccccccccccchHHHHH
Q 041414 74 KTHECSVCGLEFAIGQALGGH 94 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L~~H 94 (152)
....|..||+.|.....+..=
T Consensus 113 ~~~~C~~Cg~~f~~~k~i~~~ 133 (181)
T PRK08222 113 HLQRCSRCERPFAPQKTVALA 133 (181)
T ss_pred ccCcCcccCCccCcHhHHHHH
Confidence 578899999999977665543
No 200
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.24 E-value=68 Score=21.71 Aligned_cols=23 Identities=17% Similarity=0.351 Sum_probs=17.8
Q ss_pred CceeccccccccccchHHHHHHh
Q 041414 74 KTHECSVCGLEFAIGQALGGHMR 96 (152)
Q Consensus 74 k~~~C~~C~k~F~~~~~L~~H~~ 96 (152)
.-|.|+.||+.|...++..+-.+
T Consensus 129 ~f~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 129 EFYRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred ceeECCCCcccccCchHHHHHHH
Confidence 45789999999998887764433
No 201
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=20.17 E-value=83 Score=27.10 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=10.6
Q ss_pred eeccccccccccc
Q 041414 76 HECSVCGLEFAIG 88 (152)
Q Consensus 76 ~~C~~C~k~F~~~ 88 (152)
-.|..|++.|...
T Consensus 461 dtC~~C~kkFfSl 473 (1374)
T PTZ00303 461 DSCPSCGRAFISL 473 (1374)
T ss_pred CcccCcCCccccc
Confidence 4599999999754
No 202
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.11 E-value=84 Score=27.76 Aligned_cols=10 Identities=20% Similarity=0.869 Sum_probs=7.3
Q ss_pred ceecCccccc
Q 041414 28 AFECKTCNRQ 37 (152)
Q Consensus 28 ~~~C~~C~k~ 37 (152)
...|+.||..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4578888876
Done!