Query 021252
Match_columns 315
No_of_seqs 270 out of 1498
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 08:48:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021252.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021252hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2893 Zn finger protein [Gen 99.7 7.2E-17 1.6E-21 146.1 13.7 110 1-114 1-110 (341)
2 KOG2462 C2H2-type Zn-finger pr 99.7 7.3E-17 1.6E-21 148.9 5.3 88 13-112 163-252 (279)
3 KOG2462 C2H2-type Zn-finger pr 99.6 1.5E-15 3.2E-20 140.3 2.9 75 11-97 187-265 (279)
4 KOG3623 Homeobox transcription 99.3 3.6E-13 7.8E-18 137.1 1.3 74 11-96 894-971 (1007)
5 KOG3576 Ovo and related transc 99.3 8.7E-13 1.9E-17 117.4 0.6 77 9-97 115-195 (267)
6 KOG3576 Ovo and related transc 99.1 9.2E-12 2E-16 110.9 0.3 91 9-102 143-239 (267)
7 KOG3623 Homeobox transcription 99.1 2.8E-11 6.1E-16 123.6 0.1 72 12-95 241-329 (1007)
8 KOG1074 Transcriptional repres 98.8 1.1E-09 2.4E-14 113.6 2.1 78 10-87 352-433 (958)
9 PHA00733 hypothetical protein 98.8 5E-09 1.1E-13 88.2 4.1 77 10-100 39-124 (128)
10 KOG1074 Transcriptional repres 98.8 2E-09 4.4E-14 111.7 1.6 82 12-101 606-694 (958)
11 KOG3608 Zn finger proteins [Ge 98.6 3.7E-08 8E-13 94.2 5.6 91 9-100 261-377 (467)
12 KOG3608 Zn finger proteins [Ge 98.5 3.4E-08 7.5E-13 94.4 2.8 75 14-99 240-316 (467)
13 PHA02768 hypothetical protein; 98.5 4.5E-08 9.7E-13 70.3 2.1 41 12-52 6-48 (55)
14 PHA00733 hypothetical protein 98.4 2.6E-07 5.7E-12 77.8 4.3 51 11-61 73-125 (128)
15 PHA02768 hypothetical protein; 98.4 9.4E-08 2E-12 68.7 1.3 44 35-92 5-48 (55)
16 PLN03086 PRLI-interacting fact 98.3 1.2E-06 2.5E-11 89.8 6.6 82 12-109 454-547 (567)
17 KOG3993 Transcription factor ( 98.2 3.5E-07 7.5E-12 89.3 1.2 93 12-105 268-386 (500)
18 PHA00732 hypothetical protein 98.0 4.4E-06 9.6E-11 64.6 2.4 44 12-58 2-47 (79)
19 PHA00732 hypothetical protein 97.9 7.1E-06 1.5E-10 63.5 3.0 49 35-100 1-49 (79)
20 PHA00616 hypothetical protein 97.9 3.5E-06 7.7E-11 57.9 0.9 33 35-67 1-33 (44)
21 KOG3993 Transcription factor ( 97.6 1.6E-05 3.4E-10 78.0 0.8 53 9-61 293-382 (500)
22 PF05605 zf-Di19: Drought indu 97.6 8.4E-05 1.8E-09 53.1 3.7 46 11-59 2-53 (54)
23 PLN03086 PRLI-interacting fact 97.5 0.00013 2.9E-09 74.9 5.0 64 33-113 451-514 (567)
24 PF13465 zf-H2C2_2: Zinc-finge 97.4 7.4E-05 1.6E-09 45.6 1.1 14 50-63 1-14 (26)
25 PF13465 zf-H2C2_2: Zinc-finge 97.4 8.9E-05 1.9E-09 45.2 1.3 22 26-47 1-26 (26)
26 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00012 2.7E-09 57.1 2.1 24 76-99 51-74 (100)
27 PF00096 zf-C2H2: Zinc finger, 97.3 0.00011 2.3E-09 43.1 0.9 22 36-57 1-22 (23)
28 COG5189 SFP1 Putative transcri 97.2 9.3E-05 2E-09 70.4 0.6 65 33-97 347-420 (423)
29 PF13894 zf-C2H2_4: C2H2-type 97.2 0.00018 4E-09 41.7 1.2 24 36-59 1-24 (24)
30 PF05605 zf-Di19: Drought indu 97.1 0.00066 1.4E-08 48.5 4.0 52 35-99 2-53 (54)
31 COG5189 SFP1 Putative transcri 97.0 0.00025 5.4E-09 67.5 1.1 46 10-55 348-418 (423)
32 PHA00616 hypothetical protein 97.0 0.00037 8E-09 47.9 1.5 31 76-106 2-32 (44)
33 PF00096 zf-C2H2: Zinc finger, 96.8 0.00062 1.3E-08 39.7 1.4 21 12-32 1-21 (23)
34 PF13912 zf-C2H2_6: C2H2-type 96.8 0.00045 9.8E-09 42.0 0.7 25 35-59 1-25 (27)
35 PF09237 GAGA: GAGA factor; I 96.3 0.0016 3.5E-08 46.1 1.1 31 33-63 22-52 (54)
36 PF13894 zf-C2H2_4: C2H2-type 96.1 0.0037 8.1E-08 36.0 1.7 24 76-99 1-24 (24)
37 smart00355 ZnF_C2H2 zinc finge 96.0 0.0046 1E-07 36.0 2.0 22 36-57 1-22 (26)
38 PF12171 zf-C2H2_jaz: Zinc-fin 95.9 0.0045 9.7E-08 37.8 1.4 22 11-32 1-22 (27)
39 PF13912 zf-C2H2_6: C2H2-type 95.0 0.011 2.5E-07 35.6 1.1 25 76-100 2-26 (27)
40 smart00355 ZnF_C2H2 zinc finge 94.9 0.025 5.5E-07 32.7 2.5 24 76-99 1-24 (26)
41 PF12874 zf-met: Zinc-finger o 94.9 0.016 3.5E-07 34.3 1.6 20 13-32 2-21 (25)
42 KOG2893 Zn finger protein [Gen 94.6 0.36 7.9E-06 44.8 10.3 45 33-94 9-53 (341)
43 PF13909 zf-H2C2_5: C2H2-type 94.6 0.017 3.8E-07 34.0 1.2 24 36-60 1-24 (24)
44 PF12874 zf-met: Zinc-finger o 94.0 0.021 4.6E-07 33.8 0.7 21 36-56 1-21 (25)
45 smart00451 ZnF_U1 U1-like zinc 93.5 0.059 1.3E-06 34.3 2.2 22 11-32 3-24 (35)
46 COG5048 FOG: Zn-finger [Genera 93.0 0.039 8.4E-07 52.7 1.0 57 11-67 289-355 (467)
47 KOG1146 Homeobox protein [Gene 92.9 0.041 9E-07 61.1 1.1 84 14-97 439-540 (1406)
48 PF12171 zf-C2H2_jaz: Zinc-fin 92.7 0.047 1E-06 33.2 0.7 22 36-57 2-23 (27)
49 PRK04860 hypothetical protein; 92.6 0.054 1.2E-06 47.4 1.2 38 34-87 118-155 (160)
50 KOG2231 Predicted E3 ubiquitin 92.3 0.15 3.1E-06 53.7 4.1 23 19-41 122-146 (669)
51 KOG2231 Predicted E3 ubiquitin 92.2 0.15 3.2E-06 53.7 4.0 48 12-59 183-236 (669)
52 KOG4173 Alpha-SNAP protein [In 92.1 0.058 1.3E-06 48.9 0.8 84 12-97 80-168 (253)
53 KOG1146 Homeobox protein [Gene 90.8 0.12 2.6E-06 57.6 1.7 88 12-101 1261-1354(1406)
54 COG5048 FOG: Zn-finger [Genera 90.1 0.098 2.1E-06 49.9 0.3 67 34-112 288-360 (467)
55 PF13909 zf-H2C2_5: C2H2-type 89.1 0.27 5.8E-06 28.8 1.6 23 76-99 1-23 (24)
56 PF12756 zf-C2H2_2: C2H2 type 88.5 0.29 6.2E-06 37.7 1.8 47 13-59 1-74 (100)
57 PF09538 FYDLN_acid: Protein o 88.4 0.31 6.7E-06 39.9 2.1 35 7-48 5-39 (108)
58 PF13913 zf-C2HC_2: zinc-finge 88.3 0.3 6.5E-06 29.4 1.4 18 37-55 4-21 (25)
59 PF13913 zf-C2HC_2: zinc-finge 88.2 0.41 8.8E-06 28.8 2.0 20 12-32 3-22 (25)
60 PF09237 GAGA: GAGA factor; I 88.2 0.53 1.2E-05 33.5 2.8 29 75-103 24-52 (54)
61 COG5236 Uncharacterized conser 88.0 0.63 1.4E-05 45.4 4.1 77 12-100 221-306 (493)
62 KOG2482 Predicted C2H2-type Zn 86.8 0.32 6.9E-06 47.3 1.4 23 10-32 194-216 (423)
63 smart00451 ZnF_U1 U1-like zinc 86.3 0.46 9.9E-06 30.1 1.5 22 35-56 3-24 (35)
64 COG5236 Uncharacterized conser 85.0 0.53 1.2E-05 45.9 1.9 21 77-97 222-242 (493)
65 PF06220 zf-U1: U1 zinc finger 84.5 0.7 1.5E-05 30.7 1.8 23 10-32 2-26 (38)
66 TIGR02300 FYDLN_acid conserved 82.9 0.83 1.8E-05 38.5 2.0 39 7-52 5-43 (129)
67 COG4049 Uncharacterized protei 79.6 0.84 1.8E-05 33.1 0.8 26 7-32 12-38 (65)
68 KOG2186 Cell growth-regulating 79.4 1.1 2.4E-05 41.9 1.8 46 12-59 4-52 (276)
69 PF09986 DUF2225: Uncharacteri 76.5 0.67 1.4E-05 42.3 -0.6 39 10-48 4-61 (214)
70 PF12013 DUF3505: Protein of u 75.3 2.8 6.2E-05 33.8 2.9 27 74-100 79-109 (109)
71 KOG2482 Predicted C2H2-type Zn 71.7 3.4 7.3E-05 40.4 2.9 73 24-97 128-217 (423)
72 KOG1280 Uncharacterized conser 71.6 2.6 5.5E-05 41.2 2.0 31 69-99 73-103 (381)
73 cd00350 rubredoxin_like Rubred 69.6 3 6.6E-05 26.6 1.5 24 12-43 2-25 (33)
74 PF04959 ARS2: Arsenite-resist 69.1 1.5 3.2E-05 40.2 -0.2 31 33-63 75-105 (214)
75 PF02892 zf-BED: BED zinc fing 68.4 3.1 6.6E-05 27.9 1.4 20 36-55 17-40 (45)
76 PRK00464 nrdR transcriptional 66.1 1.6 3.6E-05 37.9 -0.5 42 13-55 2-48 (154)
77 smart00614 ZnF_BED BED zinc fi 66.0 3.9 8.6E-05 28.4 1.6 8 49-56 37-44 (50)
78 PF09986 DUF2225: Uncharacteri 65.9 2.6 5.6E-05 38.4 0.8 55 33-88 3-61 (214)
79 TIGR02098 MJ0042_CXXC MJ0042 f 65.7 2.5 5.4E-05 27.5 0.5 34 12-46 3-36 (38)
80 smart00531 TFIIE Transcription 65.6 3.3 7.2E-05 35.4 1.3 18 34-51 98-115 (147)
81 KOG4849 mRNA cleavage factor I 65.5 1.5E+02 0.0032 29.5 13.5 27 139-165 227-253 (498)
82 KOG2186 Cell growth-regulating 64.2 3.7 8E-05 38.5 1.5 18 14-32 32-49 (276)
83 PF05443 ROS_MUCR: ROS/MUCR tr 63.9 2.8 6E-05 35.6 0.5 28 33-63 70-97 (132)
84 PF13717 zinc_ribbon_4: zinc-r 63.9 3.6 7.9E-05 26.9 1.0 32 13-45 4-35 (36)
85 KOG4173 Alpha-SNAP protein [In 62.3 1.9 4.2E-05 39.2 -0.7 47 13-59 108-170 (253)
86 COG1997 RPL43A Ribosomal prote 61.4 4.1 8.8E-05 32.2 1.0 11 34-44 34-44 (89)
87 PRK00398 rpoP DNA-directed RNA 60.7 2.7 5.9E-05 28.7 -0.1 30 11-46 3-32 (46)
88 KOG3214 Uncharacterized Zn rib 59.8 4.2 9E-05 32.9 0.8 8 1-8 1-8 (109)
89 PRK04860 hypothetical protein; 59.0 6.8 0.00015 34.3 2.1 34 76-113 120-153 (160)
90 PF05191 ADK_lid: Adenylate ki 58.3 3.9 8.5E-05 26.8 0.4 33 12-48 2-34 (36)
91 KOG2932 E3 ubiquitin ligase in 58.2 1.9E+02 0.0041 28.3 16.4 21 80-100 152-172 (389)
92 COG2331 Uncharacterized protei 57.8 4.6 0.0001 31.1 0.7 31 11-45 12-43 (82)
93 PF14369 zf-RING_3: zinc-finge 56.7 5.8 0.00013 25.8 1.0 32 11-47 2-33 (35)
94 COG4957 Predicted transcriptio 56.0 5.4 0.00012 34.0 0.9 25 36-63 77-101 (148)
95 PRK06266 transcription initiat 56.0 6.4 0.00014 34.9 1.5 18 34-51 116-133 (178)
96 KOG4124 Putative transcription 55.9 2.6 5.6E-05 41.2 -1.1 64 33-96 347-419 (442)
97 PF04959 ARS2: Arsenite-resist 55.7 6.6 0.00014 36.0 1.5 24 9-32 75-98 (214)
98 PF03604 DNA_RNApol_7kD: DNA d 54.8 9.1 0.0002 24.5 1.6 26 12-44 1-26 (32)
99 smart00659 RPOLCX RNA polymera 54.5 6.7 0.00015 26.9 1.0 26 12-44 3-28 (44)
100 TIGR02605 CxxC_CxxC_SSSS putat 54.3 4 8.7E-05 28.3 -0.1 11 12-22 6-16 (52)
101 COG4530 Uncharacterized protei 54.0 8.4 0.00018 31.8 1.7 34 7-47 5-38 (129)
102 PF01286 XPA_N: XPA protein N- 53.9 5.6 0.00012 25.9 0.5 26 12-43 4-29 (34)
103 PF09723 Zn-ribbon_8: Zinc rib 53.9 3.5 7.5E-05 27.8 -0.4 11 12-22 6-16 (42)
104 PRK09678 DNA-binding transcrip 53.7 3.6 7.7E-05 31.3 -0.5 17 33-49 25-43 (72)
105 PF13719 zinc_ribbon_5: zinc-r 53.6 7.4 0.00016 25.5 1.1 33 13-46 4-36 (37)
106 PF00301 Rubredoxin: Rubredoxi 53.5 4.3 9.2E-05 28.3 -0.1 15 11-25 1-15 (47)
107 KOG3408 U1-like Zn-finger-cont 53.0 6.1 0.00013 33.1 0.8 25 34-58 56-80 (129)
108 COG1996 RPC10 DNA-directed RNA 53.0 6.8 0.00015 27.6 0.9 28 11-44 6-33 (49)
109 smart00834 CxxC_CXXC_SSSS Puta 52.7 4 8.7E-05 26.6 -0.3 11 12-22 6-16 (41)
110 PF12013 DUF3505: Protein of u 52.6 8.1 0.00018 31.1 1.5 26 35-60 80-109 (109)
111 KOG2785 C2H2-type Zn-finger pr 51.6 10 0.00022 37.5 2.2 62 36-97 167-242 (390)
112 COG4049 Uncharacterized protei 51.3 5.4 0.00012 29.0 0.2 28 33-60 15-42 (65)
113 TIGR00373 conserved hypothetic 51.0 8 0.00017 33.6 1.2 19 34-52 108-126 (158)
114 PTZ00255 60S ribosomal protein 50.9 5.6 0.00012 31.6 0.2 12 33-44 34-45 (90)
115 TIGR00622 ssl1 transcription f 50.4 16 0.00034 30.3 2.8 25 75-99 81-105 (112)
116 cd00729 rubredoxin_SM Rubredox 49.4 12 0.00025 24.2 1.5 24 12-43 3-26 (34)
117 COG1198 PriA Primosomal protei 49.0 13 0.00029 40.0 2.8 8 14-21 438-445 (730)
118 cd00730 rubredoxin Rubredoxin; 48.8 7.5 0.00016 27.4 0.6 12 12-23 2-13 (50)
119 PTZ00303 phosphatidylinositol 47.8 11 0.00023 40.9 1.7 35 13-50 462-496 (1374)
120 TIGR00280 L37a ribosomal prote 47.6 5.8 0.00013 31.5 -0.1 12 33-44 33-44 (91)
121 PRK14873 primosome assembly pr 47.3 13 0.00028 39.6 2.4 23 63-85 410-432 (665)
122 KOG2785 C2H2-type Zn-finger pr 46.4 17 0.00036 36.1 2.7 44 13-56 168-241 (390)
123 KOG4577 Transcription factor L 45.3 10 0.00022 36.4 1.0 57 10-66 32-98 (383)
124 KOG4124 Putative transcription 44.7 5.2 0.00011 39.2 -1.0 46 10-55 348-418 (442)
125 PRK04023 DNA polymerase II lar 44.3 24 0.00052 39.3 3.8 23 63-85 651-673 (1121)
126 KOG1280 Uncharacterized conser 44.2 9.5 0.00021 37.4 0.7 54 33-88 77-132 (381)
127 COG3357 Predicted transcriptio 44.1 9.6 0.00021 30.3 0.6 29 33-71 56-84 (97)
128 COG1571 Predicted DNA-binding 44.1 13 0.00029 37.4 1.7 34 10-50 349-382 (421)
129 PF01155 HypA: Hydrogenase exp 43.8 12 0.00025 30.7 1.1 26 11-44 70-95 (113)
130 PRK14890 putative Zn-ribbon RN 43.2 17 0.00036 26.7 1.7 28 11-44 7-34 (59)
131 KOG2593 Transcription initiati 42.7 14 0.00031 37.2 1.6 34 33-69 126-159 (436)
132 PF09332 Mcm10: Mcm10 replicat 42.4 7.6 0.00016 38.1 -0.3 35 13-47 254-297 (344)
133 PF01780 Ribosomal_L37ae: Ribo 42.1 6.1 0.00013 31.4 -0.8 12 33-44 33-44 (90)
134 PRK03976 rpl37ae 50S ribosomal 42.0 7.7 0.00017 30.8 -0.2 12 33-44 34-45 (90)
135 KOG1813 Predicted E3 ubiquitin 40.9 26 0.00057 33.7 3.0 58 33-98 239-302 (313)
136 PF14353 CpXC: CpXC protein 40.9 13 0.00028 30.7 0.9 44 13-56 3-59 (128)
137 PRK03824 hypA hydrogenase nick 38.6 14 0.0003 31.3 0.7 12 12-23 71-82 (135)
138 PRK11823 DNA repair protein Ra 38.3 21 0.00046 36.1 2.2 22 12-43 8-29 (446)
139 PF10571 UPF0547: Uncharacteri 38.1 20 0.00042 21.8 1.2 9 37-45 16-24 (26)
140 COG4888 Uncharacterized Zn rib 37.4 7.8 0.00017 31.4 -0.9 15 33-47 20-34 (104)
141 COG1066 Sms Predicted ATP-depe 37.2 18 0.00039 36.6 1.4 29 1-43 1-29 (456)
142 PF15168 TRIQK: Triple QxxK/R 36.8 8.7 0.00019 29.5 -0.6 22 293-314 54-75 (79)
143 COG3677 Transposase and inacti 36.7 12 0.00025 31.6 0.0 36 11-48 30-66 (129)
144 TIGR00416 sms DNA repair prote 36.4 23 0.0005 35.9 2.1 23 11-43 7-29 (454)
145 KOG3454 U1 snRNP-specific prot 36.3 15 0.00033 32.2 0.7 9 11-19 3-11 (165)
146 KOG4727 U1-like Zn-finger prot 36.3 18 0.00038 32.2 1.1 22 11-32 75-96 (193)
147 KOG2807 RNA polymerase II tran 35.8 58 0.0012 31.9 4.5 79 11-99 276-369 (378)
148 COG1773 Rubredoxin [Energy pro 35.3 14 0.00031 26.7 0.3 13 11-23 3-15 (55)
149 COG5112 UFD2 U1-like Zn-finger 35.2 14 0.00031 30.3 0.3 21 36-56 56-76 (126)
150 COG5151 SSL1 RNA polymerase II 35.1 21 0.00046 34.6 1.5 25 75-99 388-412 (421)
151 TIGR00622 ssl1 transcription f 34.4 23 0.00051 29.2 1.4 16 14-29 18-33 (112)
152 PHA00626 hypothetical protein 32.7 33 0.00071 25.0 1.8 16 74-89 22-37 (59)
153 KOG0717 Molecular chaperone (D 32.0 24 0.00052 36.0 1.3 24 9-32 290-313 (508)
154 PF05443 ROS_MUCR: ROS/MUCR tr 31.6 26 0.00057 29.7 1.4 19 11-32 72-90 (132)
155 KOG0402 60S ribosomal protein 31.6 16 0.00034 28.7 0.0 10 35-44 36-45 (92)
156 COG2888 Predicted Zn-ribbon RN 31.3 35 0.00076 25.1 1.7 33 12-50 10-42 (61)
157 PRK12380 hydrogenase nickel in 30.6 22 0.00047 29.2 0.7 10 12-21 71-80 (113)
158 COG0068 HypF Hydrogenase matur 30.3 14 0.00029 39.6 -0.7 52 14-71 126-181 (750)
159 PF13878 zf-C2H2_3: zinc-finge 30.2 45 0.00097 22.3 2.0 24 76-99 14-39 (41)
160 PF02748 PyrI_C: Aspartate car 29.8 19 0.00041 25.6 0.2 17 9-25 33-49 (52)
161 PF07754 DUF1610: Domain of un 29.1 35 0.00076 20.5 1.2 8 35-42 16-23 (24)
162 PF15269 zf-C2H2_7: Zinc-finge 28.7 35 0.00077 23.7 1.3 22 11-32 20-41 (54)
163 PRK03681 hypA hydrogenase nick 28.5 28 0.0006 28.6 1.0 10 12-21 71-80 (114)
164 KOG4167 Predicted DNA-binding 28.3 11 0.00024 40.3 -1.7 26 35-60 792-817 (907)
165 PF14446 Prok-RING_1: Prokaryo 28.2 16 0.00036 26.2 -0.4 28 12-47 6-33 (54)
166 COG5222 Uncharacterized conser 28.2 1.5E+02 0.0033 28.8 5.9 7 63-69 310-316 (427)
167 PF02176 zf-TRAF: TRAF-type zi 28.2 19 0.00041 25.3 -0.1 32 14-46 12-53 (60)
168 smart00734 ZnF_Rad18 Rad18-lik 27.8 41 0.00089 20.3 1.4 18 37-55 3-20 (26)
169 COG5188 PRP9 Splicing factor 3 27.7 25 0.00053 34.7 0.6 23 10-32 237-259 (470)
170 COG4957 Predicted transcriptio 27.4 30 0.00064 29.6 1.0 26 76-104 77-102 (148)
171 PF13240 zinc_ribbon_2: zinc-r 27.1 32 0.00069 20.2 0.8 7 14-20 2-8 (23)
172 smart00154 ZnF_AN1 AN1-like Zi 26.9 41 0.00089 22.3 1.4 13 35-47 12-24 (39)
173 cd00065 FYVE FYVE domain; Zinc 26.9 43 0.00093 23.2 1.6 26 14-47 5-30 (57)
174 KOG4215 Hepatocyte nuclear fac 26.5 19 0.00041 35.7 -0.4 17 38-55 39-55 (432)
175 TIGR03527 selenium_YedF seleni 26.1 57 0.0012 29.3 2.6 29 284-312 101-129 (194)
176 PRK00564 hypA hydrogenase nick 25.9 34 0.00074 28.2 1.0 9 13-21 73-81 (117)
177 PF01363 FYVE: FYVE zinc finge 25.7 28 0.0006 25.3 0.4 28 13-48 11-38 (69)
178 PF09845 DUF2072: Zn-ribbon co 25.4 33 0.00072 29.1 0.9 13 13-25 3-15 (131)
179 KOG2071 mRNA cleavage and poly 25.3 34 0.00073 35.8 1.1 27 76-102 419-445 (579)
180 COG4338 Uncharacterized protei 24.8 44 0.00094 23.6 1.2 14 14-27 15-28 (54)
181 TIGR00595 priA primosomal prot 24.6 50 0.0011 33.9 2.2 44 14-82 216-260 (505)
182 KOG2593 Transcription initiati 24.6 32 0.0007 34.7 0.8 36 11-46 128-164 (436)
183 PF13821 DUF4187: Domain of un 24.4 41 0.00088 24.1 1.1 19 12-30 28-46 (55)
184 TIGR00100 hypA hydrogenase nic 24.2 34 0.00073 28.1 0.7 11 36-46 71-81 (115)
185 PF07975 C1_4: TFIIH C1-like d 23.9 22 0.00047 25.3 -0.4 42 14-57 2-43 (51)
186 smart00064 FYVE Protein presen 23.6 49 0.0011 23.9 1.5 27 13-47 12-38 (68)
187 PF01927 Mut7-C: Mut7-C RNAse 23.6 47 0.001 28.2 1.6 22 75-96 124-145 (147)
188 PF02146 SIR2: Sir2 family; I 23.2 61 0.0013 28.1 2.2 30 13-43 107-137 (178)
189 PRK14873 primosome assembly pr 23.2 50 0.0011 35.3 1.9 31 13-43 385-418 (665)
190 KOG2636 Splicing factor 3a, su 22.7 63 0.0014 32.9 2.4 37 33-69 399-439 (497)
191 KOG3815 Transcription factor D 22.6 37 0.0008 32.8 0.8 44 9-53 34-80 (322)
192 PF10013 DUF2256: Uncharacteri 22.4 79 0.0017 21.6 2.1 15 14-28 11-25 (42)
193 KOG2932 E3 ubiquitin ligase in 22.2 7.6E+02 0.016 24.3 14.5 28 33-60 142-172 (389)
194 PF00412 LIM: LIM domain; Int 21.6 23 0.0005 24.5 -0.7 36 14-49 1-40 (58)
195 PF07282 OrfB_Zn_ribbon: Putat 21.1 50 0.0011 24.0 1.1 14 33-46 44-57 (69)
196 COG1656 Uncharacterized conser 20.8 77 0.0017 28.0 2.3 21 76-96 131-151 (165)
197 PF09963 DUF2197: Uncharacteri 20.4 27 0.00059 25.3 -0.5 32 12-43 3-39 (56)
198 PF04780 DUF629: Protein of un 20.1 57 0.0012 33.4 1.5 29 33-61 55-83 (466)
No 1
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=99.72 E-value=7.2e-17 Score=146.09 Aligned_cols=110 Identities=56% Similarity=1.047 Sum_probs=93.5
Q ss_pred CCCCCCCCCCccccCcCCcccCChHHHHHHhcCCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCcccccc
Q 021252 1 MGKKKKRVSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEI 80 (315)
Q Consensus 1 m~rKk~~~~eK~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~ 80 (315)
|||||++ ..|.||.||+|.|.++..|.+|++.|.|||.+|.|.+.+--.|..|..++|+|..-+++++..+|+....++
T Consensus 1 mgrkkkk-~~kpwcwycnrefddekiliqhqkakhfkchichkkl~sgpglsihcmqvhketid~ip~av~gr~~i~vei 79 (341)
T KOG2893|consen 1 MGRKKKK-VDKPWCWYCNREFDDEKILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHKETIDKIPAAVHGRDNIHVEI 79 (341)
T ss_pred CCccccc-cCCceeeecccccchhhhhhhhhhhccceeeeehhhhccCCCceeehhhhhhhhhhcccccccCCcceeEEE
Confidence 8999998 678999999999999999999999999999999999999999999999999999889999999999999999
Q ss_pred CCCCCCCHHHHHHHHhhhcCCCCccccccCCCCC
Q 021252 81 YGMQGIPPDVLAAHYGEEEEEVPSKMAKVDTSFP 114 (315)
Q Consensus 81 Cgk~F~~~s~L~~H~r~h~~e~p~k~~k~~~~~~ 114 (315)
.|+..+.+...+.-.. ++..+|..+++..+.
T Consensus 80 ygmqgip~~~~r~~~d---e~~~ekr~~~d~~~~ 110 (341)
T KOG2893|consen 80 YGMQGIPSGAYRGAAD---EEPDEKRSRMDNGPP 110 (341)
T ss_pred eeccCCCchhhhhhhh---cCchhhhhcccCCCC
Confidence 9999998866554432 233345555554443
No 2
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.66 E-value=7.3e-17 Score=148.93 Aligned_cols=88 Identities=18% Similarity=0.240 Sum_probs=78.0
Q ss_pred ccCcCCcccCChHHHHHHhc--CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCCHHH
Q 021252 13 WCYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDV 90 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~r--eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~~s~ 90 (315)
.|.+|||+|..--.|+.|+| .-+++|.+|||.|.+...|+.|+|+|+|||| |.|..|+|.|.++++
T Consensus 163 ~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKP------------F~C~hC~kAFADRSN 230 (279)
T KOG2462|consen 163 SCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKP------------FSCPHCGKAFADRSN 230 (279)
T ss_pred cCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhcccccccCCCC------------ccCCcccchhcchHH
Confidence 38888888888888888888 6688999999999999999999999999987 777889999999999
Q ss_pred HHHHHhhhcCCCCccccccCCC
Q 021252 91 LAAHYGEEEEEVPSKMAKVDTS 112 (315)
Q Consensus 91 L~~H~r~h~~e~p~k~~k~~~~ 112 (315)
|++|+++|.+.+.++|.+..-.
T Consensus 231 LRAHmQTHS~~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 231 LRAHMQTHSDVKKHQCPRCGKS 252 (279)
T ss_pred HHHHHHhhcCCccccCcchhhH
Confidence 9999999999999999887654
No 3
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.55 E-value=1.5e-15 Score=140.30 Aligned_cols=75 Identities=19% Similarity=0.295 Sum_probs=70.6
Q ss_pred ccccCcCCcccCChHHHHHHhc----CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCC
Q 021252 11 KVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGI 86 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~ 86 (315)
..+|.+|||+|++..-|+.|+| ||||.|..|+|+|..++||+.|+++|.+.|. |+|..|+|+|.
T Consensus 187 ~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~------------~qC~~C~KsFs 254 (279)
T KOG2462|consen 187 PCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKK------------HQCPRCGKSFA 254 (279)
T ss_pred CcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCcc------------ccCcchhhHHH
Confidence 4679999999999999999999 9999999999999999999999999998876 88999999999
Q ss_pred CHHHHHHHHhh
Q 021252 87 PPDVLAAHYGE 97 (315)
Q Consensus 87 ~~s~L~~H~r~ 97 (315)
..+.|.+|.+.
T Consensus 255 l~SyLnKH~ES 265 (279)
T KOG2462|consen 255 LKSYLNKHSES 265 (279)
T ss_pred HHHHHHHhhhh
Confidence 99999999754
No 4
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.32 E-value=3.6e-13 Score=137.14 Aligned_cols=74 Identities=16% Similarity=0.297 Sum_probs=69.8
Q ss_pred ccccCcCCcccCChHHHHHHhc----CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCC
Q 021252 11 KVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGI 86 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~ 86 (315)
-|-|+.|+|+|...+.|.||.- .|||+|.+|.|+|..+.+|..|+|.|.|||+ |+|+.|+|+|.
T Consensus 894 myaCDqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKP------------fQCdKClKRFS 961 (1007)
T KOG3623|consen 894 MYACDQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKP------------FQCDKCLKRFS 961 (1007)
T ss_pred cchHHHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCc------------chhhhhhhhcc
Confidence 3459999999999999999976 8999999999999999999999999999998 89999999999
Q ss_pred CHHHHHHHHh
Q 021252 87 PPDVLAAHYG 96 (315)
Q Consensus 87 ~~s~L~~H~r 96 (315)
+...+.+||.
T Consensus 962 HSGSYSQHMN 971 (1007)
T KOG3623|consen 962 HSGSYSQHMN 971 (1007)
T ss_pred cccchHhhhc
Confidence 9999999985
No 5
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.26 E-value=8.7e-13 Score=117.41 Aligned_cols=77 Identities=17% Similarity=0.264 Sum_probs=61.5
Q ss_pred CCccccCcCCcccCChHHHHHHhc----CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCC
Q 021252 9 SSKVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQ 84 (315)
Q Consensus 9 ~eK~~C~~CgK~F~~~s~Lk~H~r----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~ 84 (315)
+..+.|++|+|.|.....|.+|++ .|.|.|..|||.|...-+|+||.|+|+|.++| +|..|+|.
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpy------------kc~~c~ka 182 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPY------------KCSLCEKA 182 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCcccc------------chhhhhHH
Confidence 456779999999999999999999 78899999999999999999999999999884 44555555
Q ss_pred CCCHHHHHHHHhh
Q 021252 85 GIPPDVLAAHYGE 97 (315)
Q Consensus 85 F~~~s~L~~H~r~ 97 (315)
|.+...|+.|.+.
T Consensus 183 ftqrcsleshl~k 195 (267)
T KOG3576|consen 183 FTQRCSLESHLKK 195 (267)
T ss_pred HHhhccHHHHHHH
Confidence 5555555555443
No 6
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.13 E-value=9.2e-12 Score=110.94 Aligned_cols=91 Identities=22% Similarity=0.390 Sum_probs=76.3
Q ss_pred CCccccCcCCcccCChHHHHHHhc----CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCC--CccccccCC
Q 021252 9 SSKVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGR--ESTDIEIYG 82 (315)
Q Consensus 9 ~eK~~C~~CgK~F~~~s~Lk~H~r----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~gr--r~~~C~~Cg 82 (315)
.+++.|..|||.|.+..+|++|+| .|||+|..|+|+|.++..|..|.+.+|+... . ++..+| +-|.|+.||
T Consensus 143 vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~~-~--yaykerr~kl~vcedcg 219 (267)
T KOG3576|consen 143 VKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQH-Q--YAYKERRAKLYVCEDCG 219 (267)
T ss_pred HHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCchH-H--HHHHHhhhheeeecccC
Confidence 345679999999999999999999 8999999999999999999999999998643 1 111112 238999999
Q ss_pred CCCCCHHHHHHHHhhhcCCC
Q 021252 83 MQGIPPDVLAAHYGEEEEEV 102 (315)
Q Consensus 83 k~F~~~s~L~~H~r~h~~e~ 102 (315)
.+....+.+..|.+.|+...
T Consensus 220 ~t~~~~e~~~~h~~~~hp~S 239 (267)
T KOG3576|consen 220 YTSERPEVYYLHLKLHHPFS 239 (267)
T ss_pred CCCCChhHHHHHHHhcCCCC
Confidence 99999999999999887554
No 7
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.05 E-value=2.8e-11 Score=123.55 Aligned_cols=72 Identities=18% Similarity=0.273 Sum_probs=36.3
Q ss_pred cccCcCCcccCChHHHHHHhc-----------------CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCC
Q 021252 12 VWCYYCDREFDDEKILVQHQK-----------------AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRE 74 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r-----------------eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr 74 (315)
+.|-.|..+|..+..|.+|+. .|.|||.+|+|+|..+.+|+.|+|+|.|||+
T Consensus 241 fsC~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lRKFKCtECgKAFKfKHHLKEHlRIHSGEKP----------- 309 (1007)
T KOG3623|consen 241 FSCMLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLRKFKCTECGKAFKFKHHLKEHLRIHSGEKP----------- 309 (1007)
T ss_pred CcchhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhccccccccchhhhhHHHHHhhheeecCCCC-----------
Confidence 335555555555555555543 3445555555555555555555555555554
Q ss_pred ccccccCCCCCCCHHHHHHHH
Q 021252 75 STDIEIYGMQGIPPDVLAAHY 95 (315)
Q Consensus 75 ~~~C~~Cgk~F~~~s~L~~H~ 95 (315)
|+|..|+|+|.+...+..||
T Consensus 310 -feCpnCkKRFSHSGSySSHm 329 (1007)
T KOG3623|consen 310 -FECPNCKKRFSHSGSYSSHM 329 (1007)
T ss_pred -cCCcccccccccCCcccccc
Confidence 33344445555554444444
No 8
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.83 E-value=1.1e-09 Score=113.55 Aligned_cols=78 Identities=23% Similarity=0.416 Sum_probs=63.0
Q ss_pred CccccCcCCcccCChHHHHHHhc----CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCC
Q 021252 10 SKVWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQG 85 (315)
Q Consensus 10 eK~~C~~CgK~F~~~s~Lk~H~r----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F 85 (315)
.|.+|.+|.|.|...+.|+.|.| ||||+|.+||++|.++++|+.|...|+.+.+..--+.+++...++|++|.-.+
T Consensus 352 ~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTkGNLKvH~~rH~e~~p~~~m~p~~~~e~l~~~i~st~~ 431 (958)
T KOG1074|consen 352 FKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTKGNLKVHFQRHREKYPHVQMNPHPVQEHLQYVITSTGL 431 (958)
T ss_pred ccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccccceeeeeeeccccCCccccCCCCchhhhcceeecccc
Confidence 46679999999999999999999 99999999999999999999999777766654444445555556777776555
Q ss_pred CC
Q 021252 86 IP 87 (315)
Q Consensus 86 ~~ 87 (315)
-.
T Consensus 432 p~ 433 (958)
T KOG1074|consen 432 PY 433 (958)
T ss_pred CC
Confidence 43
No 9
>PHA00733 hypothetical protein
Probab=98.78 E-value=5e-09 Score=88.20 Aligned_cols=77 Identities=12% Similarity=0.175 Sum_probs=64.5
Q ss_pred CccccCcCCcccCChHHHHHH------hc---CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCcccccc
Q 021252 10 SKVWCYYCDREFDDEKILVQH------QK---AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEI 80 (315)
Q Consensus 10 eK~~C~~CgK~F~~~s~Lk~H------~r---eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~ 80 (315)
+++.|.+|.+.|.....|+.| +. +++|+|..|++.|.+..+|..|++.+ +.. +.|..
T Consensus 39 ~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~------------~~C~~ 104 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHS------------KVCPV 104 (128)
T ss_pred hhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcC------------ccCCC
Confidence 345699999999888777665 22 78999999999999999999999754 222 78999
Q ss_pred CCCCCCCHHHHHHHHhhhcC
Q 021252 81 YGMQGIPPDVLAAHYGEEEE 100 (315)
Q Consensus 81 Cgk~F~~~s~L~~H~r~h~~ 100 (315)
|++.|.+...|.+|++..++
T Consensus 105 CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 105 CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CCCccCCHHHHHHHHHHhcC
Confidence 99999999999999987664
No 10
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=98.77 E-value=2e-09 Score=111.70 Aligned_cols=82 Identities=23% Similarity=0.370 Sum_probs=70.2
Q ss_pred cccCcCCcccCChHHHHHHhc----CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccc---cCCCC
Q 021252 12 VWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIE---IYGMQ 84 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~---~Cgk~ 84 (315)
-+|-+|.|+.+.++.|+-|+| ||||||.+|+++|.++++|+.|+.. |+.++ +.|-.+.|. +|.+.
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~v-Hka~p-------~~R~q~ScP~~~ic~~k 677 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSV-HKAKP-------PARVQFSCPSTFICQKK 677 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccc-cccCc-------cccccccCCchhhhccc
Confidence 359999999999999999999 9999999999999999999999954 44443 123337787 99999
Q ss_pred CCCHHHHHHHHhhhcCC
Q 021252 85 GIPPDVLAAHYGEEEEE 101 (315)
Q Consensus 85 F~~~s~L~~H~r~h~~e 101 (315)
|.+.-.|.+|.++|.+.
T Consensus 678 ftn~V~lpQhIriH~~~ 694 (958)
T KOG1074|consen 678 FTNAVTLPQHIRIHLGG 694 (958)
T ss_pred ccccccccceEEeecCC
Confidence 99999999999999843
No 11
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.63 E-value=3.7e-08 Score=94.23 Aligned_cols=91 Identities=21% Similarity=0.280 Sum_probs=74.2
Q ss_pred CCccccCcCCcccCChHHHHHHhc-----CCccccccCcccCCCchhhHhHHhhhccCcccccCC--CC-----------
Q 021252 9 SSKVWCYYCDREFDDEKILVQHQK-----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPN--AK----------- 70 (315)
Q Consensus 9 ~eK~~C~~CgK~F~~~s~Lk~H~r-----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~--~~----------- 70 (315)
..-|+|..|+.+....+.|.+|+| +|+|||+.|++.|.+.+.|.+|.. .|.+..|.|.. |.
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 VNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQ-VHSKTVYQCEHPDCHYSVRTYTQMRR 339 (467)
T ss_pred hhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHH-hccccceecCCCCCcHHHHHHHHHHH
Confidence 345678889999999999999988 899999999999999999999986 55577788875 51
Q ss_pred ------C--CCCccccccCCCCCCCHHHHHHHHhhhcC
Q 021252 71 ------P--GRESTDIEIYGMQGIPPDVLAAHYGEEEE 100 (315)
Q Consensus 71 ------~--grr~~~C~~Cgk~F~~~s~L~~H~r~h~~ 100 (315)
+ ..-.|.|..|.+.|....+|.+|++..++
T Consensus 340 H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 340 HFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred HHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 1 12239999999999999999999876544
No 12
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=98.55 E-value=3.4e-08 Score=94.43 Aligned_cols=75 Identities=23% Similarity=0.407 Sum_probs=36.4
Q ss_pred cCcCCcccCChHHHHHHhc--CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCCHHHH
Q 021252 14 CYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVL 91 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~H~r--eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~~s~L 91 (315)
|..|.|.|..+..|+.|++ ...|+|..|+-+....+.|.+|+|..|. ..++++|+.|.+.|.+.++|
T Consensus 240 C~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs-----------~dkpfKCd~Cd~~c~~esdL 308 (467)
T KOG3608|consen 240 CAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHS-----------KDKPFKCDECDTRCVRESDL 308 (467)
T ss_pred HHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhc-----------cCCCccccchhhhhccHHHH
Confidence 4444444444444444443 3444444444444444444444444332 12335555666666666666
Q ss_pred HHHHhhhc
Q 021252 92 AAHYGEEE 99 (315)
Q Consensus 92 ~~H~r~h~ 99 (315)
.+|...|.
T Consensus 309 ~kH~~~HS 316 (467)
T KOG3608|consen 309 AKHVQVHS 316 (467)
T ss_pred HHHHHhcc
Confidence 66555554
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.52 E-value=4.5e-08 Score=70.34 Aligned_cols=41 Identities=17% Similarity=0.361 Sum_probs=27.6
Q ss_pred cccCcCCcccCChHHHHHHhc--CCccccccCcccCCCchhhH
Q 021252 12 VWCYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMA 52 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r--eKPfkC~~CgktF~~~~~L~ 52 (315)
|.|++|||.|.+.++|..|+| .++|+|..|++.|.+.+.|.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEYI 48 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccCCcccceecccceeE
Confidence 457777777777777777766 55677777777766666553
No 14
>PHA00733 hypothetical protein
Probab=98.41 E-value=2.6e-07 Score=77.80 Aligned_cols=51 Identities=25% Similarity=0.388 Sum_probs=47.4
Q ss_pred ccccCcCCcccCChHHHHHHhc--CCccccccCcccCCCchhhHhHHhhhccC
Q 021252 11 KVWCYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMAIHVLQVHKE 61 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r--eKPfkC~~CgktF~~~~~L~rH~r~hh~e 61 (315)
.|.|.+|++.|....+|++|++ +++|+|.+|++.|.....|.+|++..|+.
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~H~~~~h~~ 125 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLDHVCKKHNI 125 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHHHHHHhcCc
Confidence 4569999999999999999999 78999999999999999999999888864
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.40 E-value=9.4e-08 Score=68.70 Aligned_cols=44 Identities=9% Similarity=0.200 Sum_probs=37.6
Q ss_pred ccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCCHHHHH
Q 021252 35 HFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLA 92 (315)
Q Consensus 35 PfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~~s~L~ 92 (315)
-|+|++||+.|.+.++|.+|+|+|+ ++ ++|..|++.|.+.+.|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~--k~------------~kc~~C~k~f~~~s~l~ 48 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN--TN------------LKLSNCKRISLRTGEYI 48 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC--Cc------------ccCCcccceecccceeE
Confidence 4899999999999999999999987 33 67788999998776653
No 16
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.29 E-value=1.2e-06 Score=89.79 Aligned_cols=82 Identities=16% Similarity=0.220 Sum_probs=59.9
Q ss_pred cccCcCCcccCChHHHHHHhc--CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCC--
Q 021252 12 VWCYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIP-- 87 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r--eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~-- 87 (315)
+.|.+|++.|. ...|+.|++ .+++.|. |++.+ .+..|..|+++|..+++ +.|..|++.+..
T Consensus 454 ~~C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kp------------i~C~fC~~~v~~g~ 518 (567)
T PLN03086 454 VHCEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRL------------ITCRFCGDMVQAGG 518 (567)
T ss_pred ccCCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCc------------eeCCCCCCccccCc
Confidence 35999999996 678999988 7889999 99755 66899999887777776 556666666631
Q ss_pred --------HHHHHHHHhhhcCCCCcccccc
Q 021252 88 --------PDVLAAHYGEEEEEVPSKMAKV 109 (315)
Q Consensus 88 --------~s~L~~H~r~h~~e~p~k~~k~ 109 (315)
.+.|..|+..+ +.+...|..+
T Consensus 519 ~~~d~~d~~s~Lt~HE~~C-G~rt~~C~~C 547 (567)
T PLN03086 519 SAMDVRDRLRGMSEHESIC-GSRTAPCDSC 547 (567)
T ss_pred cccchhhhhhhHHHHHHhc-CCcceEcccc
Confidence 24667776664 5566666444
No 17
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.23 E-value=3.5e-07 Score=89.34 Aligned_cols=93 Identities=22% Similarity=0.321 Sum_probs=71.1
Q ss_pred cccCcCCcccCChHHHHHHhc----CCccccccCcccCCCchhhHhHHhhhccCccccc----CC-------------CC
Q 021252 12 VWCYYCDREFDDEKILVQHQK----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKV----PN-------------AK 70 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~c----p~-------------~~ 70 (315)
|.|+.|.-.|.+...|.+|.- ..-|+|.+|+|.|+-..||..|+| +|+-++..- +. ..
T Consensus 268 yiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRR-WHKPR~eaa~a~~~P~k~~~~~rae~~ea~ 346 (500)
T KOG3993|consen 268 YICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRR-WHKPRPEAAKAGSPPPKQAVETRAEVQEAE 346 (500)
T ss_pred HHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhc-ccCCchhhhhcCCCChhhhhhhhhhhhhcc
Confidence 569999999999999999976 456999999999999999999975 554332111 10 00
Q ss_pred -----CCCCccccccCCCCCCCHHHHHHHHhhhcCCCCcc
Q 021252 71 -----PGRESTDIEIYGMQGIPPDVLAAHYGEEEEEVPSK 105 (315)
Q Consensus 71 -----~grr~~~C~~Cgk~F~~~s~L~~H~r~h~~e~p~k 105 (315)
....-|.|.+|+|.|.+...|++|+-+|+.....+
T Consensus 347 rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k 386 (500)
T KOG3993|consen 347 RSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAK 386 (500)
T ss_pred ccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhccccch
Confidence 01113899999999999999999998887654433
No 18
>PHA00732 hypothetical protein
Probab=97.96 E-value=4.4e-06 Score=64.65 Aligned_cols=44 Identities=25% Similarity=0.354 Sum_probs=33.5
Q ss_pred cccCcCCcccCChHHHHHHhc--CCccccccCcccCCCchhhHhHHhhh
Q 021252 12 VWCYYCDREFDDEKILVQHQK--AKHFKCHVCHKKLSTAGGMAIHVLQV 58 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r--eKPfkC~~CgktF~~~~~L~rH~r~h 58 (315)
|.|++|++.|.+..+|++|++ ..++.|.+|+++|. .|..|.++.
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~---~l~~H~~~~ 47 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR---RLNQHFYSQ 47 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC---Chhhhhccc
Confidence 458888888888888888876 56688888888887 477777443
No 19
>PHA00732 hypothetical protein
Probab=97.92 E-value=7.1e-06 Score=63.52 Aligned_cols=49 Identities=20% Similarity=0.267 Sum_probs=40.9
Q ss_pred ccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCCHHHHHHHHhhhcC
Q 021252 35 HFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLAAHYGEEEE 100 (315)
Q Consensus 35 PfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~~s~L~~H~r~h~~ 100 (315)
+|+|..|++.|.+..+|++|++.+|.. +.|+.|++.|.+ |.+|.+++.+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~~--------------~~C~~CgKsF~~---l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHTL--------------TKCPVCNKSYRR---LNQHFYSQYD 49 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccCC--------------CccCCCCCEeCC---hhhhhcccCC
Confidence 589999999999999999999755432 468999999994 7889887655
No 20
>PHA00616 hypothetical protein
Probab=97.91 E-value=3.5e-06 Score=57.87 Aligned_cols=33 Identities=24% Similarity=0.465 Sum_probs=29.0
Q ss_pred ccccccCcccCCCchhhHhHHhhhccCcccccC
Q 021252 35 HFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVP 67 (315)
Q Consensus 35 PfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp 67 (315)
+|+|..||+.|..+.+|.+|++.||+++++.|.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~~ 33 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTLE 33 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcccee
Confidence 689999999999999999999999999875543
No 21
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=97.62 E-value=1.6e-05 Score=78.00 Aligned_cols=53 Identities=26% Similarity=0.526 Sum_probs=46.2
Q ss_pred CCccccCcCCcccCChHHHHHHhc----------------CC---------------------ccccccCcccCCCchhh
Q 021252 9 SSKVWCYYCDREFDDEKILVQHQK----------------AK---------------------HFKCHVCHKKLSTAGGM 51 (315)
Q Consensus 9 ~eK~~C~~CgK~F~~~s~Lk~H~r----------------eK---------------------PfkC~~CgktF~~~~~L 51 (315)
...|+|.+|+|.|+...+|..|+| ++ -|.|.+|+|+|.+..-|
T Consensus 293 ~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYL 372 (500)
T KOG3993|consen 293 HVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYL 372 (500)
T ss_pred EeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeecHHhhhhhHHHHHH
Confidence 346889999999999999999988 11 27899999999999999
Q ss_pred HhHHhhhccC
Q 021252 52 AIHVLQVHKE 61 (315)
Q Consensus 52 ~rH~r~hh~e 61 (315)
++|+.+|+..
T Consensus 373 rKHqlthq~~ 382 (500)
T KOG3993|consen 373 RKHQLTHQRA 382 (500)
T ss_pred HHhHHhhhcc
Confidence 9999888854
No 22
>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=97.57 E-value=8.4e-05 Score=53.12 Aligned_cols=46 Identities=28% Similarity=0.682 Sum_probs=28.3
Q ss_pred ccccCcCCcccCChHHHHHHhc------CCccccccCcccCCCchhhHhHHhhhc
Q 021252 11 KVWCYYCDREFDDEKILVQHQK------AKHFKCHVCHKKLSTAGGMAIHVLQVH 59 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r------eKPfkC~~CgktF~~~~~L~rH~r~hh 59 (315)
.|.|.+|++.| +...|..|.. .+.+.|.+|.+.+. .+|.+|++.+|
T Consensus 2 ~f~CP~C~~~~-~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKGF-SESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCcc-CHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 45677777743 3456777655 34567777776544 37777776655
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=97.46 E-value=0.00013 Score=74.94 Aligned_cols=64 Identities=14% Similarity=0.194 Sum_probs=51.7
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCCHHHHHHHHhhhcCCCCccccccCCC
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLAAHYGEEEEEVPSKMAKVDTS 112 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~~s~L~~H~r~h~~e~p~k~~k~~~~ 112 (315)
++++.|..|++.|. ...|.+|++.+| ++ +.|. ||+.+ ....|.+|+++|..+++.+|.-+...
T Consensus 451 ~~H~~C~~Cgk~f~-~s~LekH~~~~H--kp------------v~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~ 513 (567)
T PLN03086 451 KNHVHCEKCGQAFQ-QGEMEKHMKVFH--EP------------LQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDM 513 (567)
T ss_pred ccCccCCCCCCccc-hHHHHHHHHhcC--CC------------ccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCc
Confidence 46789999999996 688999998876 33 6777 88654 66899999999999999998876554
Q ss_pred C
Q 021252 113 F 113 (315)
Q Consensus 113 ~ 113 (315)
.
T Consensus 514 v 514 (567)
T PLN03086 514 V 514 (567)
T ss_pred c
Confidence 3
No 24
>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=97.37 E-value=7.4e-05 Score=45.59 Aligned_cols=14 Identities=14% Similarity=0.116 Sum_probs=8.4
Q ss_pred hhHhHHhhhccCcc
Q 021252 50 GMAIHVLQVHKENV 63 (315)
Q Consensus 50 ~L~rH~r~hh~ekp 63 (315)
+|.+|+++|.++++
T Consensus 1 ~l~~H~~~H~~~k~ 14 (26)
T PF13465_consen 1 NLRRHMRTHTGEKP 14 (26)
T ss_dssp HHHHHHHHHSSSSS
T ss_pred CHHHHhhhcCCCCC
Confidence 35666666666655
No 25
>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=97.35 E-value=8.9e-05 Score=45.23 Aligned_cols=22 Identities=36% Similarity=0.700 Sum_probs=18.2
Q ss_pred HHHHHhc----CCccccccCcccCCC
Q 021252 26 ILVQHQK----AKHFKCHVCHKKLST 47 (315)
Q Consensus 26 ~Lk~H~r----eKPfkC~~CgktF~~ 47 (315)
+|++|++ ||+|+|.+|+++|.+
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEESS
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 4666766 999999999999974
No 26
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.31 E-value=0.00012 Score=57.06 Aligned_cols=24 Identities=8% Similarity=-0.014 Sum_probs=20.8
Q ss_pred cccccCCCCCCCHHHHHHHHhhhc
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
+.|.+|++.|.....|..|++.+.
T Consensus 51 ~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 51 FRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp EEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CCCCccCCCCcCHHHHHHHHcCcc
Confidence 889999999999999999998753
No 27
>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=97.26 E-value=0.00011 Score=43.08 Aligned_cols=22 Identities=27% Similarity=0.730 Sum_probs=13.2
Q ss_pred cccccCcccCCCchhhHhHHhh
Q 021252 36 FKCHVCHKKLSTAGGMAIHVLQ 57 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r~ 57 (315)
|+|.+|++.|.++..|++|++.
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhH
Confidence 4566666666666666666554
No 28
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.22 E-value=9.3e-05 Score=70.42 Aligned_cols=65 Identities=23% Similarity=0.331 Sum_probs=48.0
Q ss_pred CCcccccc--CcccCCCchhhHhHHhhhccC-----cccccC--CCCCCCCccccccCCCCCCCHHHHHHHHhh
Q 021252 33 AKHFKCHV--CHKKLSTAGGMAIHVLQVHKE-----NVTKVP--NAKPGRESTDIEIYGMQGIPPDVLAAHYGE 97 (315)
Q Consensus 33 eKPfkC~~--CgktF~~~~~L~rH~r~hh~e-----kp~~cp--~~~~grr~~~C~~Cgk~F~~~s~L~~H~r~ 97 (315)
+|+|+|.+ |.|++.....|+-|++.-|.. .+..-+ .-....+.|+|++|+|++..-.-|+-|++-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~H 420 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRKH 420 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecccc
Confidence 79999998 999999999999998644421 110000 012245569999999999999999988764
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=97.16 E-value=0.00018 Score=41.74 Aligned_cols=24 Identities=25% Similarity=0.661 Sum_probs=15.3
Q ss_pred cccccCcccCCCchhhHhHHhhhc
Q 021252 36 FKCHVCHKKLSTAGGMAIHVLQVH 59 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r~hh 59 (315)
|+|.+|++.|.++..|++|++++|
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 567777777777777777776654
No 30
>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=97.12 E-value=0.00066 Score=48.47 Aligned_cols=52 Identities=19% Similarity=0.305 Sum_probs=40.2
Q ss_pred ccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCCHHHHHHHHhhhc
Q 021252 35 HFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 35 PfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
-|.|.+|++ ..+...|.+|....|.... +.+.|.+|...+. .+|.+|++.++
T Consensus 2 ~f~CP~C~~-~~~~~~L~~H~~~~H~~~~----------~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGK-GFSESSLVEHCEDEHRSES----------KNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCC-ccCHHHHHHHHHhHCcCCC----------CCccCCCchhhhh--hHHHHHHHHhc
Confidence 489999999 5567899999988886542 2378888987644 48999998765
No 31
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.00 E-value=0.00025 Score=67.54 Aligned_cols=46 Identities=24% Similarity=0.608 Sum_probs=41.1
Q ss_pred CccccCc--CCcccCChHHHHHHhc-----------------------CCccccccCcccCCCchhhHhHH
Q 021252 10 SKVWCYY--CDREFDDEKILVQHQK-----------------------AKHFKCHVCHKKLSTAGGMAIHV 55 (315)
Q Consensus 10 eK~~C~~--CgK~F~~~s~Lk~H~r-----------------------eKPfkC~~CgktF~~~~~L~rH~ 55 (315)
+-|+|.+ |+|+++....|+-|+. .|||+|++|+|+++....|+-|+
T Consensus 348 KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr 418 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHR 418 (423)
T ss_pred ceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhhccCccceecc
Confidence 3456987 9999999999998876 59999999999999999999996
No 32
>PHA00616 hypothetical protein
Probab=96.98 E-value=0.00037 Score=47.95 Aligned_cols=31 Identities=6% Similarity=-0.154 Sum_probs=28.5
Q ss_pred cccccCCCCCCCHHHHHHHHhhhcCCCCccc
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEEEEVPSKM 106 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~~e~p~k~ 106 (315)
|+|..||+.|.+.++|.+|++.|+++++..+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 7899999999999999999999999987654
No 33
>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=96.82 E-value=0.00062 Score=39.74 Aligned_cols=21 Identities=24% Similarity=0.566 Sum_probs=19.4
Q ss_pred cccCcCCcccCChHHHHHHhc
Q 021252 12 VWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r 32 (315)
|.|.+|++.|.+...|++|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 569999999999999999985
No 34
>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=96.78 E-value=0.00045 Score=41.95 Aligned_cols=25 Identities=24% Similarity=0.460 Sum_probs=17.1
Q ss_pred ccccccCcccCCCchhhHhHHhhhc
Q 021252 35 HFKCHVCHKKLSTAGGMAIHVLQVH 59 (315)
Q Consensus 35 PfkC~~CgktF~~~~~L~rH~r~hh 59 (315)
+|+|.+|++.|.+...|.+|++.|+
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 4667777777777777777776554
No 35
>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=96.33 E-value=0.0016 Score=46.10 Aligned_cols=31 Identities=13% Similarity=0.288 Sum_probs=23.4
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcc
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENV 63 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp 63 (315)
+.|..|.+|+..+.+..+|+||+..+|+.|+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 8899999999999999999999999998875
No 36
>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=96.07 E-value=0.0037 Score=36.02 Aligned_cols=24 Identities=17% Similarity=0.079 Sum_probs=19.9
Q ss_pred cccccCCCCCCCHHHHHHHHhhhc
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
|.|.+|++.|.....|++|+++|+
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 579999999999999999998864
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.04 E-value=0.0046 Score=35.99 Aligned_cols=22 Identities=18% Similarity=0.563 Sum_probs=14.7
Q ss_pred cccccCcccCCCchhhHhHHhh
Q 021252 36 FKCHVCHKKLSTAGGMAIHVLQ 57 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r~ 57 (315)
|+|..|++.|.....|.+|++.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~ 22 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRT 22 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHH
Confidence 4566777777777777777653
No 38
>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=95.86 E-value=0.0045 Score=37.77 Aligned_cols=22 Identities=41% Similarity=0.789 Sum_probs=16.1
Q ss_pred ccccCcCCcccCChHHHHHHhc
Q 021252 11 KVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r 32 (315)
+|+|..|+|.|.....|++|++
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCCcccCCCCcCCHHHHHHHHc
Confidence 3667788888888877777765
No 39
>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=94.99 E-value=0.011 Score=35.64 Aligned_cols=25 Identities=12% Similarity=0.001 Sum_probs=22.8
Q ss_pred cccccCCCCCCCHHHHHHHHhhhcC
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEEE 100 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~~ 100 (315)
+.|..|++.|.....|.+|++.|..
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCccCCccCChhHHHHHhHHhcC
Confidence 7899999999999999999988753
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=94.94 E-value=0.025 Score=32.70 Aligned_cols=24 Identities=13% Similarity=-0.011 Sum_probs=21.5
Q ss_pred cccccCCCCCCCHHHHHHHHhhhc
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
++|..|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 468999999999999999999765
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.92 E-value=0.016 Score=34.30 Aligned_cols=20 Identities=35% Similarity=0.851 Sum_probs=11.3
Q ss_pred ccCcCCcccCChHHHHHHhc
Q 021252 13 WCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~r 32 (315)
+|+.|++.|.....|+.|++
T Consensus 2 ~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCcCCHHHHHHHHC
Confidence 45555555555555555544
No 42
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=94.64 E-value=0.36 Score=44.81 Aligned_cols=45 Identities=16% Similarity=0.232 Sum_probs=31.2
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCCHHHHHHH
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIPPDVLAAH 94 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~~s~L~~H 94 (315)
.|+| |=+|++.|-...-|..|++. |. |+|.+|.|.....--|..|
T Consensus 9 ~kpw-cwycnrefddekiliqhqka----kh------------fkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 9 DKPW-CWYCNREFDDEKILIQHQKA----KH------------FKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred CCce-eeecccccchhhhhhhhhhh----cc------------ceeeeehhhhccCCCceee
Confidence 5665 88999999999999988753 33 6677777665444444433
No 43
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.61 E-value=0.017 Score=33.98 Aligned_cols=24 Identities=25% Similarity=0.527 Sum_probs=14.9
Q ss_pred cccccCcccCCCchhhHhHHhhhcc
Q 021252 36 FKCHVCHKKLSTAGGMAIHVLQVHK 60 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r~hh~ 60 (315)
|+|..|..... +..|.+|++.+|+
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHHS
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhCc
Confidence 56777776666 6677777776653
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.02 E-value=0.021 Score=33.76 Aligned_cols=21 Identities=29% Similarity=0.767 Sum_probs=12.9
Q ss_pred cccccCcccCCCchhhHhHHh
Q 021252 36 FKCHVCHKKLSTAGGMAIHVL 56 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r 56 (315)
|.|.+|++.|.+...|+.|++
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~ 21 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR 21 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT
T ss_pred CCCCCCCCCcCCHHHHHHHHC
Confidence 456666666666666666654
No 45
>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=93.53 E-value=0.059 Score=34.31 Aligned_cols=22 Identities=32% Similarity=0.649 Sum_probs=15.6
Q ss_pred ccccCcCCcccCChHHHHHHhc
Q 021252 11 KVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r 32 (315)
+++|++|++.|.....++.|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4567777777777777777765
No 46
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=93.02 E-value=0.039 Score=52.66 Aligned_cols=57 Identities=23% Similarity=0.400 Sum_probs=49.1
Q ss_pred ccccCcCCcccCChHHHHHHhc------C--Cccccc--cCcccCCCchhhHhHHhhhccCcccccC
Q 021252 11 KVWCYYCDREFDDEKILVQHQK------A--KHFKCH--VCHKKLSTAGGMAIHVLQVHKENVTKVP 67 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r------e--KPfkC~--~CgktF~~~~~L~rH~r~hh~ekp~~cp 67 (315)
.+.|..|.+.|.+...|.+|.+ + +++.|. .|++.|.+.+.+.+|.++|.+.+..++.
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCccccc
Confidence 3569999999999999998877 6 999999 7999999999999999988876655543
No 47
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=92.91 E-value=0.041 Score=61.08 Aligned_cols=84 Identities=13% Similarity=0.171 Sum_probs=63.0
Q ss_pred cCcCCcccCChHHHHHHhc-----CCccccccCcccCCCchhhHhHHhhhccCcc-cccC----CCC--------CCCCc
Q 021252 14 CYYCDREFDDEKILVQHQK-----AKHFKCHVCHKKLSTAGGMAIHVLQVHKENV-TKVP----NAK--------PGRES 75 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~H~r-----eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp-~~cp----~~~--------~grr~ 75 (315)
|.-|+..+.++..+..|+. .|-|+|.+|+..|.....|..|+|..|-+-. ..|. .+. -++..
T Consensus 439 ~~~~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p 518 (1406)
T KOG1146|consen 439 LTKAEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKP 518 (1406)
T ss_pred ccchhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccccccccccCCCCc
Confidence 5556777777777777766 7889999999999999999999998664321 1111 111 12345
Q ss_pred cccccCCCCCCCHHHHHHHHhh
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGE 97 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~ 97 (315)
|.|+.|...+....+|.+|++.
T Consensus 519 ~~C~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 519 YPCRACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccceeeeeeeecchHHHHHHHH
Confidence 8999999999999999999876
No 48
>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=92.68 E-value=0.047 Score=33.15 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=16.6
Q ss_pred cccccCcccCCCchhhHhHHhh
Q 021252 36 FKCHVCHKKLSTAGGMAIHVLQ 57 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r~ 57 (315)
|.|..|++.|.+...|..|++.
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 6678888888888888777654
No 49
>PRK04860 hypothetical protein; Provisional
Probab=92.57 E-value=0.054 Score=47.40 Aligned_cols=38 Identities=18% Similarity=0.225 Sum_probs=25.8
Q ss_pred CccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCccccccCCCCCCC
Q 021252 34 KHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDIEIYGMQGIP 87 (315)
Q Consensus 34 KPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C~~Cgk~F~~ 87 (315)
-+|+|. |++ ....+++|.+.|.+++. |.|..|++.|..
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g~~~------------YrC~~C~~~l~~ 155 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRGEAV------------YRCRRCGETLVF 155 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcCCcc------------EECCCCCceeEE
Confidence 357786 776 66777888877777765 566666665543
No 50
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.29 E-value=0.15 Score=53.74 Aligned_cols=23 Identities=30% Similarity=0.602 Sum_probs=14.2
Q ss_pred cccCChHHHHHHhc--CCccccccC
Q 021252 19 REFDDEKILVQHQK--AKHFKCHVC 41 (315)
Q Consensus 19 K~F~~~s~Lk~H~r--eKPfkC~~C 41 (315)
-.|....+|++|++ -+-+.|.+|
T Consensus 122 ~~~~s~~~Lk~H~~~~H~~~~c~lC 146 (669)
T KOG2231|consen 122 TEFKSVENLKNHMRDQHKLHLCSLC 146 (669)
T ss_pred cchhHHHHHHHHHHHhhhhhccccc
Confidence 33447788899987 344555554
No 51
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.19 E-value=0.15 Score=53.69 Aligned_cols=48 Identities=25% Similarity=0.536 Sum_probs=34.5
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCc------ccCCCchhhHhHHhhhc
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCH------KKLSTAGGMAIHVLQVH 59 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cg------ktF~~~~~L~rH~r~hh 59 (315)
..|.+|...|-....|.+|++...|.|.+|. .-|..-+.|..|.|..|
T Consensus 183 p~C~~C~~~fld~~el~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 183 PLCKFCHERFLDDDELYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred ccchhhhhhhccHHHHHHhhccceeheeecCcccccchhcccchHHHHHhhhcC
Confidence 4588888888888888888886677777773 33556677777777655
No 52
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.08 E-value=0.058 Score=48.87 Aligned_cols=84 Identities=17% Similarity=0.205 Sum_probs=61.9
Q ss_pred cccCc--CCcccCChHHHHHHhc-CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCCcccc--ccCCCCCC
Q 021252 12 VWCYY--CDREFDDEKILVQHQK-AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRESTDI--EIYGMQGI 86 (315)
Q Consensus 12 ~~C~~--CgK~F~~~s~Lk~H~r-eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr~~~C--~~Cgk~F~ 86 (315)
+.|++ |-+.|+...++..|.. ..--.|.+|.+.|-+...|..|+...|..- |... ...|.+-|+| +.|+..|.
T Consensus 80 ~~cqvagc~~~~d~lD~~E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI~E~HDs~-Fqa~-veRG~dMy~ClvEgCt~KFk 157 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALDDYEHHYHTLHGNSCSFCKRAFPTGHLLDAHILEWHDSL-FQAL-VERGQDMYQCLVEGCTEKFK 157 (253)
T ss_pred ccccccchHHHHhhhhhHHHhhhhcccchhHHHHHhCCchhhhhHHHHHHHHHH-HHHH-HHcCccHHHHHHHhhhhhhh
Confidence 45887 8888988888888877 444589999999999999999997777421 0000 0112344777 78999999
Q ss_pred CHHHHHHHHhh
Q 021252 87 PPDVLAAHYGE 97 (315)
Q Consensus 87 ~~s~L~~H~r~ 97 (315)
...+.+.|+-.
T Consensus 158 T~r~RkdH~I~ 168 (253)
T KOG4173|consen 158 TSRDRKDHMIR 168 (253)
T ss_pred hhhhhhhHHHH
Confidence 99898999744
No 53
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=90.85 E-value=0.12 Score=57.65 Aligned_cols=88 Identities=10% Similarity=0.083 Sum_probs=66.2
Q ss_pred cccCcCCcccCChHHHHHHhc-CCccccccCcccCCCchhhHhHHhhhcc-Ccc--ccc--CCCCCCCCccccccCCCCC
Q 021252 12 VWCYYCDREFDDEKILVQHQK-AKHFKCHVCHKKLSTAGGMAIHVLQVHK-ENV--TKV--PNAKPGRESTDIEIYGMQG 85 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r-eKPfkC~~CgktF~~~~~L~rH~r~hh~-ekp--~~c--p~~~~grr~~~C~~Cgk~F 85 (315)
+.|..|++.|.-...+. |+- +++|+|.+|...|.....|..|.+.... .+. ..- +...+.++.| |.+|...|
T Consensus 1261 ~~c~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~l~~~~~k~~~~~~~~~~~~~~~l~~~d~~~~-c~~c~~~~ 1338 (1406)
T KOG1146|consen 1261 GECGAVDELLTPSFGIS-TLDVTHRYLCRQCKMAFDGEAPLTAHQRKFCFAGRGSGGSMPPPLRVPDCTYH-CLACEVLL 1338 (1406)
T ss_pred chhhhccccccCcccee-ecccchhHHHHHHHhhhcchhHHHHHHHHHHhccCccccCCCCcccCcccccc-chHHHhhc
Confidence 55999999999988888 887 9999999999999999999999843210 000 000 0112334447 99999999
Q ss_pred CCHHHHHHHHhhhcCC
Q 021252 86 IPPDVLAAHYGEEEEE 101 (315)
Q Consensus 86 ~~~s~L~~H~r~h~~e 101 (315)
.....|..|||+.+.+
T Consensus 1339 ~~~~alqihm~~~~~~ 1354 (1406)
T KOG1146|consen 1339 SGREALQIHMRSSAHR 1354 (1406)
T ss_pred chhHHHHHHHHHhhhc
Confidence 9999999999985543
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.08 E-value=0.098 Score=49.87 Aligned_cols=67 Identities=18% Similarity=0.166 Sum_probs=54.2
Q ss_pred CccccccCcccCCCchhhHhHHh--hhccC--cccccCCCCCCCCccccc--cCCCCCCCHHHHHHHHhhhcCCCCcccc
Q 021252 34 KHFKCHVCHKKLSTAGGMAIHVL--QVHKE--NVTKVPNAKPGRESTDIE--IYGMQGIPPDVLAAHYGEEEEEVPSKMA 107 (315)
Q Consensus 34 KPfkC~~CgktF~~~~~L~rH~r--~hh~e--kp~~cp~~~~grr~~~C~--~Cgk~F~~~s~L~~H~r~h~~e~p~k~~ 107 (315)
..+.|..|...|.+...|.+|.+ .|.++ ++ +.|. .|++.|.+...+++|...|.+....++.
T Consensus 288 ~~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~------------~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (467)
T COG5048 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKP------------FSCPYSLCGKLFSRNDALKRHILLHTSISPAKEK 355 (467)
T ss_pred cCCCCccccCCccccccccccccccccccccCCc------------eeeeccCCCccccccccccCCcccccCCCccccc
Confidence 47999999999999999999999 67777 55 4454 7999999999999999999877655554
Q ss_pred ccCCC
Q 021252 108 KVDTS 112 (315)
Q Consensus 108 k~~~~ 112 (315)
-....
T Consensus 356 ~~~~~ 360 (467)
T COG5048 356 LLNSS 360 (467)
T ss_pred cccCc
Confidence 44333
No 55
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=89.10 E-value=0.27 Score=28.76 Aligned_cols=23 Identities=9% Similarity=-0.018 Sum_probs=18.0
Q ss_pred cccccCCCCCCCHHHHHHHHhhhc
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
|+|..|..... ...|++|++.++
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 57889998887 889999999875
No 56
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=88.45 E-value=0.29 Score=37.75 Aligned_cols=47 Identities=30% Similarity=0.695 Sum_probs=22.2
Q ss_pred ccCcCCcccCChHHHHHHhc---------------------------CCccccccCcccCCCchhhHhHHhhhc
Q 021252 13 WCYYCDREFDDEKILVQHQK---------------------------AKHFKCHVCHKKLSTAGGMAIHVLQVH 59 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~r---------------------------eKPfkC~~CgktF~~~~~L~rH~r~hh 59 (315)
+|.+|+..|.....|..|++ ...+.|.+|++.|.....|..|++.++
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~~~~l~~~~~~~~~~~~~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPDQKYLVDPNRLLNYLRKKVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred CccccccccccccccccccccccccccccccccccccccccccccccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 48899999999988888875 235899999999999999999998763
No 57
>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=88.41 E-value=0.31 Score=39.94 Aligned_cols=35 Identities=20% Similarity=0.461 Sum_probs=28.0
Q ss_pred CCCCccccCcCCcccCChHHHHHHhcCCccccccCcccCCCc
Q 021252 7 RVSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTA 48 (315)
Q Consensus 7 ~~~eK~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~ 48 (315)
..|.|..|..||+.|-... ..|-.|.+||..|.-.
T Consensus 5 elGtKR~Cp~CG~kFYDLn-------k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 5 ELGTKRTCPSCGAKFYDLN-------KDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCcccCCCCcchhccCC-------CCCccCCCCCCccCcc
Confidence 3466778999999995433 5788999999999876
No 58
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=88.26 E-value=0.3 Score=29.41 Aligned_cols=18 Identities=22% Similarity=0.659 Sum_probs=8.3
Q ss_pred ccccCcccCCCchhhHhHH
Q 021252 37 KCHVCHKKLSTAGGMAIHV 55 (315)
Q Consensus 37 kC~~CgktF~~~~~L~rH~ 55 (315)
.|..|+++| ..+.|.+|+
T Consensus 4 ~C~~CgR~F-~~~~l~~H~ 21 (25)
T PF13913_consen 4 PCPICGRKF-NPDRLEKHE 21 (25)
T ss_pred cCCCCCCEE-CHHHHHHHH
Confidence 344455554 334444443
No 59
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=88.17 E-value=0.41 Score=28.82 Aligned_cols=20 Identities=40% Similarity=0.748 Sum_probs=16.6
Q ss_pred cccCcCCcccCChHHHHHHhc
Q 021252 12 VWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r 32 (315)
..|..|||.| ....|.+|++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~ 22 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEK 22 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHH
Confidence 3599999999 6777899974
No 60
>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=88.16 E-value=0.53 Score=33.50 Aligned_cols=29 Identities=17% Similarity=0.087 Sum_probs=21.5
Q ss_pred ccccccCCCCCCCHHHHHHHHhhhcCCCC
Q 021252 75 STDIEIYGMQGIPPDVLAAHYGEEEEEVP 103 (315)
Q Consensus 75 ~~~C~~Cgk~F~~~s~L~~H~r~h~~e~p 103 (315)
.-.|.+|+..+.+..+|++|++.+++.++
T Consensus 24 PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 24 PATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp -EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred CCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 36789999999999999999999887654
No 61
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=88.01 E-value=0.63 Score=45.39 Aligned_cols=77 Identities=19% Similarity=0.333 Sum_probs=49.2
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcc-------cCCCchhhHhHHhhhccCcccccC--CCCCCCCccccccCC
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHK-------KLSTAGGMAIHVLQVHKENVTKVP--NAKPGRESTDIEIYG 82 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgk-------tF~~~~~L~rH~r~hh~ekp~~cp--~~~~grr~~~C~~Cg 82 (315)
+.|.+|.+.|-+...|.+|.|++.-+|.+|++ -|..-..|.+|.+.-| |.|- .|..+ .|
T Consensus 221 P~C~FC~~~FYdDDEL~~HcR~~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~h----y~ct~qtc~~~-------k~- 288 (493)
T COG5236 221 PLCIFCKIYFYDDDELRRHCRLRHEACHICDMVGPIRYQYFKSYEDLEAHFRNAH----YCCTFQTCRVG-------KC- 288 (493)
T ss_pred chhhhccceecChHHHHHHHHhhhhhhhhhhccCccchhhhhCHHHHHHHhhcCc----eEEEEEEEecC-------cE-
Confidence 35999999999999999999955555555543 3777788888875333 2221 11111 11
Q ss_pred CCCCCHHHHHHHHhhhcC
Q 021252 83 MQGIPPDVLAAHYGEEEE 100 (315)
Q Consensus 83 k~F~~~s~L~~H~r~h~~ 100 (315)
..|...-.|..|....++
T Consensus 289 ~vf~~~~el~~h~~~~h~ 306 (493)
T COG5236 289 YVFPYHTELLEHLTRFHK 306 (493)
T ss_pred EEeccHHHHHHHHHHHhh
Confidence 347777788888755443
No 62
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=86.84 E-value=0.32 Score=47.28 Aligned_cols=23 Identities=30% Similarity=0.885 Sum_probs=20.4
Q ss_pred CccccCcCCcccCChHHHHHHhc
Q 021252 10 SKVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 10 eK~~C~~CgK~F~~~s~Lk~H~r 32 (315)
++..|-+|.|.|..+..|+.|||
T Consensus 194 ~r~~CLyCekifrdkntLkeHMr 216 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMR 216 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHH
Confidence 35679999999999999999998
No 63
>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=86.33 E-value=0.46 Score=30.08 Aligned_cols=22 Identities=18% Similarity=0.522 Sum_probs=15.1
Q ss_pred ccccccCcccCCCchhhHhHHh
Q 021252 35 HFKCHVCHKKLSTAGGMAIHVL 56 (315)
Q Consensus 35 PfkC~~CgktF~~~~~L~rH~r 56 (315)
.|.|++|++.|.....+..|++
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~ 24 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLK 24 (35)
T ss_pred CeEccccCCccCCHHHHHHHHC
Confidence 4667777777777777776664
No 64
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=84.97 E-value=0.53 Score=45.88 Aligned_cols=21 Identities=14% Similarity=-0.118 Sum_probs=11.3
Q ss_pred ccccCCCCCCCHHHHHHHHhh
Q 021252 77 DIEIYGMQGIPPDVLAAHYGE 97 (315)
Q Consensus 77 ~C~~Cgk~F~~~s~L~~H~r~ 97 (315)
.|..|...|.+.+.|.+|+|.
T Consensus 222 ~C~FC~~~FYdDDEL~~HcR~ 242 (493)
T COG5236 222 LCIFCKIYFYDDDELRRHCRL 242 (493)
T ss_pred hhhhccceecChHHHHHHHHh
Confidence 355555555555555555554
No 65
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=84.52 E-value=0.7 Score=30.71 Aligned_cols=23 Identities=30% Similarity=0.794 Sum_probs=10.7
Q ss_pred CccccCcCCcccC-Ch-HHHHHHhc
Q 021252 10 SKVWCYYCDREFD-DE-KILVQHQK 32 (315)
Q Consensus 10 eK~~C~~CgK~F~-~~-s~Lk~H~r 32 (315)
.||+|++|++.|. +. ...+.|.+
T Consensus 2 ~ryyCdyC~~~~~~d~~~~Rk~H~~ 26 (38)
T PF06220_consen 2 PRYYCDYCKKYLTHDSPSIRKQHER 26 (38)
T ss_dssp -S-B-TTT--B-S--SHHHHHHHT-
T ss_pred cCeecccccceecCCChHHHHHhhc
Confidence 3688999999993 33 45577866
No 66
>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=82.86 E-value=0.83 Score=38.45 Aligned_cols=39 Identities=10% Similarity=0.152 Sum_probs=29.5
Q ss_pred CCCCccccCcCCcccCChHHHHHHhcCCccccccCcccCCCchhhH
Q 021252 7 RVSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMA 52 (315)
Q Consensus 7 ~~~eK~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~~~L~ 52 (315)
..|.|..|..||+.|-... ..|-.|.+||..|.....++
T Consensus 5 elGtKr~Cp~cg~kFYDLn-------k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDLN-------RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred hhCccccCCCcCccccccC-------CCCccCCCcCCccCcchhhc
Confidence 3466778999999995433 57899999999987664443
No 67
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=79.57 E-value=0.84 Score=33.09 Aligned_cols=26 Identities=23% Similarity=0.433 Sum_probs=17.7
Q ss_pred CCCCccc-cCcCCcccCChHHHHHHhc
Q 021252 7 RVSSKVW-CYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 7 ~~~eK~~-C~~CgK~F~~~s~Lk~H~r 32 (315)
+++|.+. |..||+.|.+..++.+|..
T Consensus 12 RDGE~~lrCPRC~~~FR~~K~Y~RHVN 38 (65)
T COG4049 12 RDGEEFLRCPRCGMVFRRRKDYIRHVN 38 (65)
T ss_pred cCCceeeeCCchhHHHHHhHHHHHHhh
Confidence 4566553 7777777777777777755
No 68
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=79.41 E-value=1.1 Score=41.87 Aligned_cols=46 Identities=17% Similarity=0.341 Sum_probs=32.5
Q ss_pred cccCcCCcccCChHHHHHHhc---CCccccccCcccCCCchhhHhHHhhhc
Q 021252 12 VWCYYCDREFDDEKILVQHQK---AKHFKCHVCHKKLSTAGGMAIHVLQVH 59 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~r---eKPfkC~~CgktF~~~~~L~rH~r~hh 59 (315)
|.|..||-.... -.+.+|+. ..-|.|..|++.|.+ ...+.|....+
T Consensus 4 FtCnvCgEsvKK-p~vekH~srCrn~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESVKK-PQVEKHMSRCRNAYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhccc-cchHHHHHhccCCeeEEeeccccccc-chhhhhhhhcc
Confidence 348888876543 45666876 667888888888888 77777775443
No 69
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=76.45 E-value=0.67 Score=42.29 Aligned_cols=39 Identities=21% Similarity=0.438 Sum_probs=28.1
Q ss_pred CccccCcCCcccCChHHHHHHhc-------------------CCccccccCcccCCCc
Q 021252 10 SKVWCYYCDREFDDEKILVQHQK-------------------AKHFKCHVCHKKLSTA 48 (315)
Q Consensus 10 eK~~C~~CgK~F~~~s~Lk~H~r-------------------eKPfkC~~CgktF~~~ 48 (315)
++..|.+|++.|..+..+....| -.-+.|..||.+|...
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 35679999999988876665554 1224799999887755
No 70
>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=75.26 E-value=2.8 Score=33.76 Aligned_cols=27 Identities=11% Similarity=0.165 Sum_probs=24.1
Q ss_pred Ccccc----ccCCCCCCCHHHHHHHHhhhcC
Q 021252 74 ESTDI----EIYGMQGIPPDVLAAHYGEEEE 100 (315)
Q Consensus 74 r~~~C----~~Cgk~F~~~s~L~~H~r~h~~ 100 (315)
+.|.| ..|+........+++|.+.+++
T Consensus 79 ~G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 79 DGYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CCeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 56899 9999999999999999998764
No 71
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=71.69 E-value=3.4 Score=40.39 Aligned_cols=73 Identities=21% Similarity=0.281 Sum_probs=45.6
Q ss_pred hHHHHHHhc---CC--ccccccCcccCC-CchhhHhHHhhhccCcccccCCC-----------CCCCCccccccCCCCCC
Q 021252 24 EKILVQHQK---AK--HFKCHVCHKKLS-TAGGMAIHVLQVHKENVTKVPNA-----------KPGRESTDIEIYGMQGI 86 (315)
Q Consensus 24 ~s~Lk~H~r---eK--PfkC~~CgktF~-~~~~L~rH~r~hh~ekp~~cp~~-----------~~grr~~~C~~Cgk~F~ 86 (315)
+..|.+|++ ++ .-+|..|+.-+. .++....|.-..|+-.. .-+.. +..-.+.+|-.|.|.|.
T Consensus 128 ~eaLeqqQ~Eredt~fslqClFCn~e~lgnRs~~l~Hlf~~H~lni-GlpDniVyvnelLehLkekL~r~~CLyCekifr 206 (423)
T KOG2482|consen 128 KEALEQQQKEREDTIFSLQCLFCNNEGLGNRSEILEHLFHVHGLNI-GLPDNIVYVNELLEHLKEKLERLRCLYCEKIFR 206 (423)
T ss_pred HHHHHHHHHHhcCCeeeeEEEEecchhcccHHHHHHHHHHHhhhcc-CCCcceeeHHHHHHHHHHHHhhheeeeeccccC
Confidence 345666766 23 346999986553 44556667655554221 11110 11112388999999999
Q ss_pred CHHHHHHHHhh
Q 021252 87 PPDVLAAHYGE 97 (315)
Q Consensus 87 ~~s~L~~H~r~ 97 (315)
++..|+.|||.
T Consensus 207 dkntLkeHMrk 217 (423)
T KOG2482|consen 207 DKNTLKEHMRK 217 (423)
T ss_pred CcHHHHHHHHh
Confidence 99999999986
No 72
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=71.61 E-value=2.6 Score=41.19 Aligned_cols=31 Identities=13% Similarity=0.175 Sum_probs=22.2
Q ss_pred CCCCCCccccccCCCCCCCHHHHHHHHhhhc
Q 021252 69 AKPGRESTDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 69 ~~~grr~~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
+....+.|.|.+|++....+..+..|....+
T Consensus 73 ~~y~~qSftCPyC~~~Gfte~~f~~Hv~s~H 103 (381)
T KOG1280|consen 73 SHYDPQSFTCPYCGIMGFTERQFGTHVLSQH 103 (381)
T ss_pred cccccccccCCcccccccchhHHHHHhhhcC
Confidence 3334446888888888888888888876544
No 73
>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=69.64 E-value=3 Score=26.57 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=13.3
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcc
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgk 43 (315)
|.|..||..+... +.+++|.+|+.
T Consensus 2 ~~C~~CGy~y~~~--------~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGE--------EAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCC--------cCCCcCcCCCC
Confidence 4566676554322 24666666653
No 74
>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=69.12 E-value=1.5 Score=40.24 Aligned_cols=31 Identities=23% Similarity=0.520 Sum_probs=24.2
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcc
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENV 63 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp 63 (315)
+..|.|.+|+|.|.-..-.++|+...|.|+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~v 105 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPEKV 105 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHHHH
Confidence 4568999999999999999999999888763
No 75
>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=68.38 E-value=3.1 Score=27.90 Aligned_cols=20 Identities=25% Similarity=0.571 Sum_probs=8.3
Q ss_pred cccccCcccCCCc----hhhHhHH
Q 021252 36 FKCHVCHKKLSTA----GGMAIHV 55 (315)
Q Consensus 36 fkC~~CgktF~~~----~~L~rH~ 55 (315)
.+|.+|++.+... ++|.+|+
T Consensus 17 a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 17 AKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp EEETTTTEE-----SSTHHHHHHH
T ss_pred EEeCCCCeEEeeCCCcHHHHHHhh
Confidence 4455555544432 4555555
No 76
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=66.12 E-value=1.6 Score=37.93 Aligned_cols=42 Identities=14% Similarity=0.343 Sum_probs=25.6
Q ss_pred ccCcCCcccCC--hH-HHHH--HhcCCccccccCcccCCCchhhHhHH
Q 021252 13 WCYYCDREFDD--EK-ILVQ--HQKAKHFKCHVCHKKLSTAGGMAIHV 55 (315)
Q Consensus 13 ~C~~CgK~F~~--~s-~Lk~--H~reKPfkC~~CgktF~~~~~L~rH~ 55 (315)
+|.+||-.+.. .+ .+.. +. .|.++|..||++|.+-..+..-+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~-~~~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAI-RRRRECLACGKRFTTFERVELVP 48 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCce-eeeeeccccCCcceEeEeccCcc
Confidence 59999965521 11 1111 11 34489999999998776655433
No 77
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=65.96 E-value=3.9 Score=28.35 Aligned_cols=8 Identities=13% Similarity=0.260 Sum_probs=4.7
Q ss_pred hhhHhHHh
Q 021252 49 GGMAIHVL 56 (315)
Q Consensus 49 ~~L~rH~r 56 (315)
++|.+|++
T Consensus 37 s~L~rHl~ 44 (50)
T smart00614 37 SNLRRHLR 44 (50)
T ss_pred HHHHHHHH
Confidence 46666655
No 78
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=65.91 E-value=2.6 Score=38.42 Aligned_cols=55 Identities=18% Similarity=0.197 Sum_probs=32.6
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCC----CCccccccCCCCCCCH
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPG----RESTDIEIYGMQGIPP 88 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~g----rr~~~C~~Cgk~F~~~ 88 (315)
+|..+|.+|++.|.++.-+.+..|....+.- -|+.-... -.-..|..||.++...
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D-~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSD-FCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCC-CccccCCCCCeeeeEEECCCCCCccccc
Confidence 4678999999999988777666654332211 12210000 0114688999887644
No 79
>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=65.73 E-value=2.5 Score=27.47 Aligned_cols=34 Identities=15% Similarity=0.362 Sum_probs=19.7
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcccCC
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLS 46 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~ 46 (315)
..|..|+..|.-....... .....+|..|+..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~-~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGA-NGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCC-CCCEEECCCCCCEEE
Confidence 4577788777665543211 123467777776653
No 80
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=65.61 E-value=3.3 Score=35.39 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=12.1
Q ss_pred CccccccCcccCCCchhh
Q 021252 34 KHFKCHVCHKKLSTAGGM 51 (315)
Q Consensus 34 KPfkC~~CgktF~~~~~L 51 (315)
.-|.|..|++.|.....+
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~ 115 (147)
T smart00531 98 AYYKCPNCQSKYTFLEAN 115 (147)
T ss_pred cEEECcCCCCEeeHHHHH
Confidence 357788888877754443
No 81
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=65.47 E-value=1.5e+02 Score=29.47 Aligned_cols=27 Identities=19% Similarity=0.195 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021252 139 QPIYSSAVPVPPAGWPVPPRPQPWYPQ 165 (315)
Q Consensus 139 ~P~~~p~~p~p~~~~~~P~~P~p~~p~ 165 (315)
.|.+.+....|+-....|+++-..+-|
T Consensus 227 ~P~m~~P~s~P~N~~~~P~~~~Q~~Gq 253 (498)
T KOG4849|consen 227 TPLMSQPTSLPSNLNQAPQMRLQINGQ 253 (498)
T ss_pred CCCCCCCCCCCCCcCcCcccCcCcCCC
Confidence 455665555555555666665544433
No 82
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=64.24 E-value=3.7 Score=38.50 Aligned_cols=18 Identities=28% Similarity=0.672 Sum_probs=8.9
Q ss_pred cCcCCcccCChHHHHHHhc
Q 021252 14 CYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~H~r 32 (315)
|-.|++.|.+ ..++.|..
T Consensus 32 CIDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 32 CIDCGKTFER-VSYKNHTK 49 (276)
T ss_pred Eeeccccccc-chhhhhhh
Confidence 5555555554 34445544
No 83
>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=63.91 E-value=2.8 Score=35.61 Aligned_cols=28 Identities=25% Similarity=0.367 Sum_probs=17.7
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcc
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENV 63 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp 63 (315)
+.-..|.+|||.|.. |+||.+.|||-.+
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred cCeeEEccCCcccch---HHHHHHHccCCCH
Confidence 445679999999875 5999999988654
No 84
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=63.89 E-value=3.6 Score=26.85 Aligned_cols=32 Identities=16% Similarity=0.542 Sum_probs=18.7
Q ss_pred ccCcCCcccCChHHHHHHhcCCccccccCcccC
Q 021252 13 WCYYCDREFDDEKILVQHQKAKHFKCHVCHKKL 45 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF 45 (315)
.|..|++.|.-...... .+.+..+|..|+..|
T Consensus 4 ~Cp~C~~~y~i~d~~ip-~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIP-PKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCC-CCCcEEECCCCCCEe
Confidence 47777777766554321 114456677777665
No 85
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.28 E-value=1.9 Score=39.23 Aligned_cols=47 Identities=28% Similarity=0.673 Sum_probs=39.3
Q ss_pred ccCcCCcccCChHHHHHHhc-----------CC---cccccc--CcccCCCchhhHhHHhhhc
Q 021252 13 WCYYCDREFDDEKILVQHQK-----------AK---HFKCHV--CHKKLSTAGGMAIHVLQVH 59 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~r-----------eK---PfkC~~--CgktF~~~~~L~rH~r~hh 59 (315)
.|.+|.|.|....-|..|+. || -|+|-+ |+..|.+...-++|+-..|
T Consensus 108 sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 108 SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 49999999999999999876 44 488976 9999999988888875444
No 86
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=61.43 E-value=4.1 Score=32.16 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=6.0
Q ss_pred CccccccCccc
Q 021252 34 KHFKCHVCHKK 44 (315)
Q Consensus 34 KPfkC~~Cgkt 44 (315)
..|.|..|++.
T Consensus 34 ~~~~Cp~C~~~ 44 (89)
T COG1997 34 AKHVCPFCGRT 44 (89)
T ss_pred cCCcCCCCCCc
Confidence 34566666544
No 87
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=60.68 E-value=2.7 Score=28.67 Aligned_cols=30 Identities=20% Similarity=0.542 Sum_probs=19.0
Q ss_pred ccccCcCCcccCChHHHHHHhcCCccccccCcccCC
Q 021252 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLS 46 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~ 46 (315)
.|.|..||..|..... ...++|..||..+.
T Consensus 3 ~y~C~~CG~~~~~~~~------~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEY------GTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCC------CCceECCCCCCeEE
Confidence 3568888877754332 22677888876554
No 88
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=59.79 E-value=4.2 Score=32.91 Aligned_cols=8 Identities=50% Similarity=0.866 Sum_probs=4.7
Q ss_pred CCCCCCCC
Q 021252 1 MGKKKKRV 8 (315)
Q Consensus 1 m~rKk~~~ 8 (315)
|||||.+.
T Consensus 1 MgkRk~K~ 8 (109)
T KOG3214|consen 1 MGKRKSKR 8 (109)
T ss_pred CCcccccc
Confidence 66666543
No 89
>PRK04860 hypothetical protein; Provisional
Probab=58.97 E-value=6.8 Score=34.26 Aligned_cols=34 Identities=6% Similarity=-0.032 Sum_probs=29.1
Q ss_pred cccccCCCCCCCHHHHHHHHhhhcCCCCccccccCCCC
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEEEEVPSKMAKVDTSF 113 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~~e~p~k~~k~~~~~ 113 (315)
|.|. |++ ....+++|.++|.++..++|.++....
T Consensus 120 Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 120 YRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCcee
Confidence 8898 987 667889999999999999998876654
No 90
>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=58.30 E-value=3.9 Score=26.83 Aligned_cols=33 Identities=21% Similarity=0.253 Sum_probs=20.0
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcccCCCc
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTA 48 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~ 48 (315)
..|..||+.|....+-- ...-+|+.||..+.++
T Consensus 2 r~C~~Cg~~Yh~~~~pP----~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPP----KVEGVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEEETTTB------SSTTBCTTTTEBEBEE
T ss_pred cCcCCCCCccccccCCC----CCCCccCCCCCeeEeC
Confidence 34888888875433210 4556788888766554
No 91
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=58.20 E-value=1.9e+02 Score=28.29 Aligned_cols=21 Identities=14% Similarity=-0.045 Sum_probs=16.4
Q ss_pred cCCCCCCCHHHHHHHHhhhcC
Q 021252 80 IYGMQGIPPDVLAAHYGEEEE 100 (315)
Q Consensus 80 ~Cgk~F~~~s~L~~H~r~h~~ 100 (315)
.|.++|....+|.+|....++
T Consensus 152 GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 152 GCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred hHHHHHhhHHHHHHHhhhhhc
Confidence 588899999999999765443
No 92
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.79 E-value=4.6 Score=31.08 Aligned_cols=31 Identities=26% Similarity=0.548 Sum_probs=23.0
Q ss_pred ccccCcCCcccCChHHHHHHhcCCcc-ccccCcccC
Q 021252 11 KVWCYYCDREFDDEKILVQHQKAKHF-KCHVCHKKL 45 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~reKPf-kC~~CgktF 45 (315)
.|.|..|+..| .+.+|+++-|+ .|+.|+-.|
T Consensus 12 ~Y~c~~cg~~~----dvvq~~~ddplt~ce~c~a~~ 43 (82)
T COG2331 12 SYECTECGNRF----DVVQAMTDDPLTTCEECGARL 43 (82)
T ss_pred EEeecccchHH----HHHHhcccCccccChhhChHH
Confidence 45699999776 67888885554 699997644
No 93
>PF14369 zf-RING_3: zinc-finger
Probab=56.69 E-value=5.8 Score=25.82 Aligned_cols=32 Identities=22% Similarity=0.578 Sum_probs=20.1
Q ss_pred ccccCcCCcccCChHHHHHHhcCCccccccCcccCCC
Q 021252 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLST 47 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~ 47 (315)
.|+|..|++...-... ....-.|..|+..|..
T Consensus 2 ~ywCh~C~~~V~~~~~-----~~~~~~CP~C~~gFvE 33 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPS-----PDSDVACPRCHGGFVE 33 (35)
T ss_pred CEeCccCCCEeEeCcC-----CCCCcCCcCCCCcEeE
Confidence 4789999987753221 0111259999888864
No 94
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=55.99 E-value=5.4 Score=34.03 Aligned_cols=25 Identities=16% Similarity=0.109 Sum_probs=20.8
Q ss_pred cccccCcccCCCchhhHhHHhhhccCcc
Q 021252 36 FKCHVCHKKLSTAGGMAIHVLQVHKENV 63 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r~hh~ekp 63 (315)
..|.+|||.|. .|+||.++|++-.+
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCH
Confidence 36889999997 69999999998655
No 95
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.97 E-value=6.4 Score=34.92 Aligned_cols=18 Identities=28% Similarity=0.621 Sum_probs=13.4
Q ss_pred CccccccCcccCCCchhh
Q 021252 34 KHFKCHVCHKKLSTAGGM 51 (315)
Q Consensus 34 KPfkC~~CgktF~~~~~L 51 (315)
.-|.|..|+++|+.-+.+
T Consensus 116 ~~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAM 133 (178)
T ss_pred CEEECCCCCcEEeHHHHh
Confidence 457888888888777665
No 96
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=55.85 E-value=2.6 Score=41.25 Aligned_cols=64 Identities=23% Similarity=0.305 Sum_probs=43.2
Q ss_pred CCcccccc--CcccCCCchhhHhHHhhhccC---cccccCCC----CCCCCccccccCCCCCCCHHHHHHHHh
Q 021252 33 AKHFKCHV--CHKKLSTAGGMAIHVLQVHKE---NVTKVPNA----KPGRESTDIEIYGMQGIPPDVLAAHYG 96 (315)
Q Consensus 33 eKPfkC~~--CgktF~~~~~L~rH~r~hh~e---kp~~cp~~----~~grr~~~C~~Cgk~F~~~s~L~~H~r 96 (315)
+++|+|.+ |.+.++....|+.|...-|.. .+.+++.. .-..+.|+|++|.+++.....|+-|..
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCceee
Confidence 89999987 999999988999887544421 11122211 123566999999998876666665543
No 97
>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=55.67 E-value=6.6 Score=36.02 Aligned_cols=24 Identities=21% Similarity=0.432 Sum_probs=19.2
Q ss_pred CCccccCcCCcccCChHHHHHHhc
Q 021252 9 SSKVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 9 ~eK~~C~~CgK~F~~~s~Lk~H~r 32 (315)
..||.|..|+|.|.-..-.++|+.
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~ 98 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIF 98 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHh
Confidence 447889999999999999999987
No 98
>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=54.77 E-value=9.1 Score=24.50 Aligned_cols=26 Identities=19% Similarity=0.531 Sum_probs=14.0
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCccc
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgkt 44 (315)
|.|..||..+..+. ..+.+|..||.+
T Consensus 1 Y~C~~Cg~~~~~~~-------~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVELKP-------GDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-BST-------SSTSSBSSSS-S
T ss_pred CCCCcCCCeeEcCC-------CCcEECCcCCCe
Confidence 35777777665222 335567777654
No 99
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=54.51 E-value=6.7 Score=26.88 Aligned_cols=26 Identities=23% Similarity=0.523 Sum_probs=15.5
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCccc
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgkt 44 (315)
|.|..||..|..+. ....+|..||..
T Consensus 3 Y~C~~Cg~~~~~~~-------~~~irC~~CG~r 28 (44)
T smart00659 3 YICGECGRENEIKS-------KDVVRCRECGYR 28 (44)
T ss_pred EECCCCCCEeecCC-------CCceECCCCCce
Confidence 55777777665431 345667777654
No 100
>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=54.32 E-value=4 Score=28.30 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=6.1
Q ss_pred cccCcCCcccC
Q 021252 12 VWCYYCDREFD 22 (315)
Q Consensus 12 ~~C~~CgK~F~ 22 (315)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (52)
T TIGR02605 6 YRCTACGHRFE 16 (52)
T ss_pred EEeCCCCCEeE
Confidence 34666666554
No 101
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.98 E-value=8.4 Score=31.76 Aligned_cols=34 Identities=12% Similarity=0.027 Sum_probs=25.8
Q ss_pred CCCCccccCcCCcccCChHHHHHHhcCCccccccCcccCCC
Q 021252 7 RVSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLST 47 (315)
Q Consensus 7 ~~~eK~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~ 47 (315)
..+.|-.|..|+|.|-... .+|..|.+||++|-+
T Consensus 5 eLGtKridPetg~KFYDLN-------rdPiVsPytG~s~P~ 38 (129)
T COG4530 5 ELGTKRIDPETGKKFYDLN-------RDPIVSPYTGKSYPR 38 (129)
T ss_pred cccccccCccccchhhccC-------CCccccCcccccchH
Confidence 3455666999999985433 679999999999943
No 102
>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=53.94 E-value=5.6 Score=25.92 Aligned_cols=26 Identities=31% Similarity=0.620 Sum_probs=11.8
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcc
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgk 43 (315)
..|.+|++.|..+.- -+.|.+.+|.+
T Consensus 4 ~~C~eC~~~f~dSyL------~~~F~~~VCD~ 29 (34)
T PF01286_consen 4 PKCDECGKPFMDSYL------LNNFDLPVCDK 29 (34)
T ss_dssp EE-TTT--EES-SSC------CCCTS-S--TT
T ss_pred chHhHhCCHHHHHHH------HHhCCcccccc
Confidence 458888888876653 44566666654
No 103
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=53.90 E-value=3.5 Score=27.78 Aligned_cols=11 Identities=36% Similarity=0.875 Sum_probs=6.0
Q ss_pred cccCcCCcccC
Q 021252 12 VWCYYCDREFD 22 (315)
Q Consensus 12 ~~C~~CgK~F~ 22 (315)
|+|..||..|.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 34666665553
No 104
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=53.71 E-value=3.6 Score=31.34 Aligned_cols=17 Identities=18% Similarity=0.454 Sum_probs=8.4
Q ss_pred CCccccc--cCcccCCCch
Q 021252 33 AKHFKCH--VCHKKLSTAG 49 (315)
Q Consensus 33 eKPfkC~--~CgktF~~~~ 49 (315)
++-++|. .||.+|....
T Consensus 25 ~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 25 ERYHQCQNVNCSATFITYE 43 (72)
T ss_pred eeeeecCCCCCCCEEEEEE
Confidence 4445555 4555555433
No 105
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=53.59 E-value=7.4 Score=25.46 Aligned_cols=33 Identities=15% Similarity=0.409 Sum_probs=19.2
Q ss_pred ccCcCCcccCChHHHHHHhcCCccccccCcccCC
Q 021252 13 WCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLS 46 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~ 46 (315)
.|..|+..|.-..+... ...+..+|..|+..|.
T Consensus 4 ~CP~C~~~f~v~~~~l~-~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLP-AGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcc-cCCcEEECCCCCcEee
Confidence 47777777766554211 1145667777776653
No 106
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=53.53 E-value=4.3 Score=28.31 Aligned_cols=15 Identities=40% Similarity=0.678 Sum_probs=8.3
Q ss_pred ccccCcCCcccCChH
Q 021252 11 KVWCYYCDREFDDEK 25 (315)
Q Consensus 11 K~~C~~CgK~F~~~s 25 (315)
||.|..|+..+.-..
T Consensus 1 ky~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEK 15 (47)
T ss_dssp EEEETTTSBEEETTT
T ss_pred CcCCCCCCEEEcCCc
Confidence 355666666654443
No 107
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=53.00 E-value=6.1 Score=33.07 Aligned_cols=25 Identities=20% Similarity=0.398 Sum_probs=19.3
Q ss_pred CccccccCcccCCCchhhHhHHhhh
Q 021252 34 KHFKCHVCHKKLSTAGGMAIHVLQV 58 (315)
Q Consensus 34 KPfkC~~CgktF~~~~~L~rH~r~h 58 (315)
-.|-|-+|.+-|.....|..|.++.
T Consensus 56 GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 56 GQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred ceeehhhhhhhhcchHHHHHHHhcc
Confidence 3477888888888888888887654
No 108
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=52.96 E-value=6.8 Score=27.64 Aligned_cols=28 Identities=21% Similarity=0.667 Sum_probs=17.2
Q ss_pred ccccCcCCcccCChHHHHHHhcCCccccccCccc
Q 021252 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgkt 44 (315)
.|.|-.||+.|.... ......|..||.+
T Consensus 6 ~Y~C~~Cg~~~~~~~------~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVELDQ------ETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeeehhh------ccCceeCCCCCcE
Confidence 356888888872221 1556678888754
No 109
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=52.74 E-value=4 Score=26.63 Aligned_cols=11 Identities=27% Similarity=0.761 Sum_probs=6.3
Q ss_pred cccCcCCcccC
Q 021252 12 VWCYYCDREFD 22 (315)
Q Consensus 12 ~~C~~CgK~F~ 22 (315)
|+|..||+.|.
T Consensus 6 y~C~~Cg~~fe 16 (41)
T smart00834 6 YRCEDCGHTFE 16 (41)
T ss_pred EEcCCCCCEEE
Confidence 34666666554
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=52.62 E-value=8.1 Score=31.07 Aligned_cols=26 Identities=19% Similarity=0.327 Sum_probs=23.5
Q ss_pred cccc----ccCcccCCCchhhHhHHhhhcc
Q 021252 35 HFKC----HVCHKKLSTAGGMAIHVLQVHK 60 (315)
Q Consensus 35 PfkC----~~CgktF~~~~~L~rH~r~hh~ 60 (315)
-|.| ..|+....+...+.+|.+.+|+
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 4789 8999999999999999998885
No 111
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=51.57 E-value=10 Score=37.52 Aligned_cols=62 Identities=13% Similarity=0.063 Sum_probs=44.7
Q ss_pred cccccCcccCCCchhhHhHHhhhccCcccccCCC-----------CCCCCccccccCC---CCCCCHHHHHHHHhh
Q 021252 36 FKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNA-----------KPGRESTDIEIYG---MQGIPPDVLAAHYGE 97 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~-----------~~grr~~~C~~Cg---k~F~~~s~L~~H~r~ 97 (315)
--|..|++.|.+-..-.+|+..+|+-.--.-... ......+.|..|. +.|..-...++||+.
T Consensus 167 t~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 167 TDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred cceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 4588999999999999999988887432111111 1122347788887 899999999999975
No 112
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=51.33 E-value=5.4 Score=29.00 Aligned_cols=28 Identities=18% Similarity=0.367 Sum_probs=24.3
Q ss_pred CCccccccCcccCCCchhhHhHHhhhcc
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHK 60 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ 60 (315)
|-=++|..|+.-|....+..+|...-|+
T Consensus 15 E~~lrCPRC~~~FR~~K~Y~RHVNKaH~ 42 (65)
T COG4049 15 EEFLRCPRCGMVFRRRKDYIRHVNKAHG 42 (65)
T ss_pred ceeeeCCchhHHHHHhHHHHHHhhHHhh
Confidence 6668999999999999999999876665
No 113
>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=51.04 E-value=8 Score=33.59 Aligned_cols=19 Identities=16% Similarity=0.272 Sum_probs=14.0
Q ss_pred CccccccCcccCCCchhhH
Q 021252 34 KHFKCHVCHKKLSTAGGMA 52 (315)
Q Consensus 34 KPfkC~~CgktF~~~~~L~ 52 (315)
.=|.|..|+.+|+....+.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~ 126 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME 126 (158)
T ss_pred CeEECCCCCcEeeHHHHHH
Confidence 4477888888887777764
No 114
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=50.91 E-value=5.6 Score=31.61 Aligned_cols=12 Identities=25% Similarity=0.711 Sum_probs=8.3
Q ss_pred CCccccccCccc
Q 021252 33 AKHFKCHVCHKK 44 (315)
Q Consensus 33 eKPfkC~~Cgkt 44 (315)
...|.|..|++.
T Consensus 34 ~a~y~CpfCgk~ 45 (90)
T PTZ00255 34 HAKYFCPFCGKH 45 (90)
T ss_pred hCCccCCCCCCC
Confidence 556788888654
No 115
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.45 E-value=16 Score=30.25 Aligned_cols=25 Identities=4% Similarity=-0.334 Sum_probs=19.8
Q ss_pred ccccccCCCCCCCHHHHHHHHhhhc
Q 021252 75 STDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 75 ~~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
+|+|..|...|-.+-+.-.|+..|.
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred ceeCCCCCCccccccchhhhhhccC
Confidence 3889999999988878888876664
No 116
>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=49.41 E-value=12 Score=24.17 Aligned_cols=24 Identities=25% Similarity=0.508 Sum_probs=12.6
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcc
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgk 43 (315)
|.|..||..+... +.|.+|.+|+.
T Consensus 3 ~~C~~CG~i~~g~--------~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGE--------EAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECC--------cCCCcCcCCCC
Confidence 4466666554221 24556666653
No 117
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.00 E-value=13 Score=39.97 Aligned_cols=8 Identities=25% Similarity=0.488 Sum_probs=5.7
Q ss_pred cCcCCccc
Q 021252 14 CYYCDREF 21 (315)
Q Consensus 14 C~~CgK~F 21 (315)
|..||..+
T Consensus 438 C~~Cg~v~ 445 (730)
T COG1198 438 CRDCGYIA 445 (730)
T ss_pred cccCCCcc
Confidence 77777655
No 118
>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=48.80 E-value=7.5 Score=27.43 Aligned_cols=12 Identities=25% Similarity=0.551 Sum_probs=6.8
Q ss_pred cccCcCCcccCC
Q 021252 12 VWCYYCDREFDD 23 (315)
Q Consensus 12 ~~C~~CgK~F~~ 23 (315)
|.|..||..+.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 456666655553
No 119
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=47.81 E-value=11 Score=40.92 Aligned_cols=35 Identities=20% Similarity=0.318 Sum_probs=21.8
Q ss_pred ccCcCCcccCChHHHHHHhcCCccccccCcccCCCchh
Q 021252 13 WCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGG 50 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~~~ 50 (315)
.|..|++.|.....+ .-.|.+-|..||+.|.....
T Consensus 462 tC~~C~kkFfSlsK~---L~~RKHHCRkCGrVFC~~CS 496 (1374)
T PTZ00303 462 SCPSCGRAFISLSRP---LGTRAHHCRSCGIRLCVFCI 496 (1374)
T ss_pred cccCcCCcccccccc---cccccccccCCccccCcccc
Confidence 399999999653110 01355678888887765543
No 120
>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=47.56 E-value=5.8 Score=31.54 Aligned_cols=12 Identities=33% Similarity=0.838 Sum_probs=7.7
Q ss_pred CCccccccCccc
Q 021252 33 AKHFKCHVCHKK 44 (315)
Q Consensus 33 eKPfkC~~Cgkt 44 (315)
...|.|..|++.
T Consensus 33 ~a~y~CpfCgk~ 44 (91)
T TIGR00280 33 KAKYVCPFCGKK 44 (91)
T ss_pred hcCccCCCCCCC
Confidence 456777777644
No 121
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.26 E-value=13 Score=39.64 Aligned_cols=23 Identities=4% Similarity=-0.091 Sum_probs=14.3
Q ss_pred ccccCCCCCCCCccccccCCCCC
Q 021252 63 VTKVPNAKPGRESTDIEIYGMQG 85 (315)
Q Consensus 63 p~~cp~~~~grr~~~C~~Cgk~F 85 (315)
...|..|........|..||...
T Consensus 410 ~l~Ch~CG~~~~p~~Cp~Cgs~~ 432 (665)
T PRK14873 410 TPRCRWCGRAAPDWRCPRCGSDR 432 (665)
T ss_pred eeECCCCcCCCcCccCCCCcCCc
Confidence 34677764433456788887653
No 122
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=46.42 E-value=17 Score=36.11 Aligned_cols=44 Identities=20% Similarity=0.483 Sum_probs=37.7
Q ss_pred ccCcCCcccCChHHHHHHhc---------------------------CCccccccCc---ccCCCchhhHhHHh
Q 021252 13 WCYYCDREFDDEKILVQHQK---------------------------AKHFKCHVCH---KKLSTAGGMAIHVL 56 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~r---------------------------eKPfkC~~Cg---ktF~~~~~L~rH~r 56 (315)
.|-+|++.|..-..-..|+. .+-|.|..|. +.|.+-...+.|++
T Consensus 168 ~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~ 241 (390)
T KOG2785|consen 168 DCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMR 241 (390)
T ss_pred ceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHh
Confidence 49999999998888888876 4567899998 99999999999985
No 123
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=45.29 E-value=10 Score=36.39 Aligned_cols=57 Identities=21% Similarity=0.388 Sum_probs=35.6
Q ss_pred CccccCcCCcccCChHHHHHHhc---CCccccccCc-----ccCCCchhh--HhHHhhhccCccccc
Q 021252 10 SKVWCYYCDREFDDEKILVQHQK---AKHFKCHVCH-----KKLSTAGGM--AIHVLQVHKENVTKV 66 (315)
Q Consensus 10 eK~~C~~CgK~F~~~s~Lk~H~r---eKPfkC~~Cg-----ktF~~~~~L--~rH~r~hh~ekp~~c 66 (315)
+...|.-|++-..++..|+.-.| .+-.+|..|. +.|.+.+.+ +.|.-..-|-|...|
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC 98 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSAC 98 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhh
Confidence 45679999988877777765544 6666777774 567777665 334333334443333
No 124
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=44.73 E-value=5.2 Score=39.21 Aligned_cols=46 Identities=26% Similarity=0.632 Sum_probs=36.1
Q ss_pred CccccCc--CCcccCChHHHHHHhc-----------------------CCccccccCcccCCCchhhHhHH
Q 021252 10 SKVWCYY--CDREFDDEKILVQHQK-----------------------AKHFKCHVCHKKLSTAGGMAIHV 55 (315)
Q Consensus 10 eK~~C~~--CgK~F~~~s~Lk~H~r-----------------------eKPfkC~~CgktF~~~~~L~rH~ 55 (315)
+-|+|.+ |+|.++....|+.|.. .|+|+|++|.++++....|+-|+
T Consensus 348 ~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~s~~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~~ 418 (442)
T KOG4124|consen 348 KPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTPTPAPIPHQGFVVENKPYRCEVCSKRYKNLNGLKYHR 418 (442)
T ss_pred CCCCCCCCcchhhcccCcceeeccccCcCCCCCCCCCCCCCcceeeeccCcccChhhhhhhccCCCCCcee
Confidence 3456865 9999988888877643 68899999999888888887775
No 125
>PRK04023 DNA polymerase II large subunit; Validated
Probab=44.33 E-value=24 Score=39.28 Aligned_cols=23 Identities=22% Similarity=0.255 Sum_probs=13.0
Q ss_pred ccccCCCCCCCCccccccCCCCC
Q 021252 63 VTKVPNAKPGRESTDIEIYGMQG 85 (315)
Q Consensus 63 p~~cp~~~~grr~~~C~~Cgk~F 85 (315)
.+.|+.|......+.|..||..-
T Consensus 651 i~fCP~CG~~~~~y~CPKCG~El 673 (1121)
T PRK04023 651 VYRCPRCGIEVEEDECEKCGREP 673 (1121)
T ss_pred ceeCccccCcCCCCcCCCCCCCC
Confidence 34666664433346677777543
No 126
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=44.18 E-value=9.5 Score=37.37 Aligned_cols=54 Identities=22% Similarity=0.212 Sum_probs=36.4
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCccc--ccCCCCCCCCccccccCCCCCCCH
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVT--KVPNAKPGRESTDIEIYGMQGIPP 88 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~--~cp~~~~grr~~~C~~Cgk~F~~~ 88 (315)
+.-|.|.+|++.=.+...|..|+...|.+-.+ .|+.|-... ..|.+|.|.-...
T Consensus 77 ~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~icp~c~~~~--~~qp~~~~~~~~~ 132 (381)
T KOG1280|consen 77 PQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVICPLCAANP--EMQPIHSKETENL 132 (381)
T ss_pred cccccCCcccccccchhHHHHHhhhcCcccCcceeeeccccCc--ccCchhhhhhhhh
Confidence 56799999999988889999999888876542 344443222 4455555544433
No 127
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=44.13 E-value=9.6 Score=30.34 Aligned_cols=29 Identities=14% Similarity=0.469 Sum_probs=19.2
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcccccCCCCC
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKP 71 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~ 71 (315)
.+|-+|..||..|.. +-+ +++..||.|+.
T Consensus 56 v~Pa~CkkCGfef~~-~~i---------k~pSRCP~CKS 84 (97)
T COG3357 56 VRPARCKKCGFEFRD-DKI---------KKPSRCPKCKS 84 (97)
T ss_pred ecChhhcccCccccc-ccc---------CCcccCCcchh
Confidence 578889999888876 221 24556777653
No 128
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=44.10 E-value=13 Score=37.38 Aligned_cols=34 Identities=15% Similarity=0.359 Sum_probs=22.2
Q ss_pred CccccCcCCcccCChHHHHHHhcCCccccccCcccCCCchh
Q 021252 10 SKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGG 50 (315)
Q Consensus 10 eK~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~~~ 50 (315)
+++.|..||+.-.+.- ..-|+|..|++++.....
T Consensus 349 ~~p~Cp~Cg~~m~S~G-------~~g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 349 VNPVCPRCGGRMKSAG-------RNGFRCKKCGTRARETLI 382 (421)
T ss_pred cCCCCCccCCchhhcC-------CCCcccccccccCCcccc
Confidence 3567888887643322 227888888888765443
No 129
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=43.80 E-value=12 Score=30.68 Aligned_cols=26 Identities=27% Similarity=0.811 Sum_probs=14.6
Q ss_pred ccccCcCCcccCChHHHHHHhcCCccccccCccc
Q 021252 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgkt 44 (315)
+.+|..||+.|..... .+.|..|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~--------~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEF--------DFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECHHC--------CHH-SSSSSS
T ss_pred cEECCCCCCEEecCCC--------CCCCcCCcCC
Confidence 3457778777755442 2567777654
No 130
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=43.25 E-value=17 Score=26.68 Aligned_cols=28 Identities=25% Similarity=0.455 Sum_probs=16.6
Q ss_pred ccccCcCCcccCChHHHHHHhcCCccccccCccc
Q 021252 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKK 44 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgkt 44 (315)
+.+|.-||+...-... .-.|.|..||+.
T Consensus 7 ~~~CtSCg~~i~~~~~------~~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIEIAPREK------AVKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCcccCCCc------cCEeeCCCCCCe
Confidence 3457777765432211 345788888776
No 131
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=42.67 E-value=14 Score=37.16 Aligned_cols=34 Identities=15% Similarity=0.339 Sum_probs=22.7
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcccccCCC
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNA 69 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~ 69 (315)
..-|+|..|.++|..-..++. .-....-|.|..|
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L---~~~~~~~F~C~~C 159 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQL---LDNETGEFHCENC 159 (436)
T ss_pred cccccCCccccchhhhHHHHh---hcccCceEEEecC
Confidence 467999999999998777652 2222334566665
No 132
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=42.44 E-value=7.6 Score=38.13 Aligned_cols=35 Identities=20% Similarity=0.362 Sum_probs=14.7
Q ss_pred ccCcCCcccCChHHHH---HHhc------CCccccccCcccCCC
Q 021252 13 WCYYCDREFDDEKILV---QHQK------AKHFKCHVCHKKLST 47 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk---~H~r------eKPfkC~~CgktF~~ 47 (315)
.|..|.++......+- .|.- .|=|+|..|+++...
T Consensus 254 ~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~s 297 (344)
T PF09332_consen 254 TCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTIS 297 (344)
T ss_dssp EETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEE
T ss_pred EcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeee
Confidence 3788877765555443 2322 344778888776443
No 133
>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=42.14 E-value=6.1 Score=31.37 Aligned_cols=12 Identities=25% Similarity=0.791 Sum_probs=7.4
Q ss_pred CCccccccCccc
Q 021252 33 AKHFKCHVCHKK 44 (315)
Q Consensus 33 eKPfkC~~Cgkt 44 (315)
...|.|..|++.
T Consensus 33 ~~ky~Cp~Cgk~ 44 (90)
T PF01780_consen 33 HAKYTCPFCGKT 44 (90)
T ss_dssp HS-BEESSSSSS
T ss_pred hCCCcCCCCCCc
Confidence 456777777654
No 134
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=41.99 E-value=7.7 Score=30.82 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=7.9
Q ss_pred CCccccccCccc
Q 021252 33 AKHFKCHVCHKK 44 (315)
Q Consensus 33 eKPfkC~~Cgkt 44 (315)
...|.|..|++.
T Consensus 34 ~a~y~CpfCgk~ 45 (90)
T PRK03976 34 RAKHVCPVCGRP 45 (90)
T ss_pred hcCccCCCCCCC
Confidence 456777777654
No 135
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.86 E-value=26 Score=33.69 Aligned_cols=58 Identities=19% Similarity=0.156 Sum_probs=36.6
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccCcccccCCC--CCCCCccccccCCCC----CCCHHHHHHHHhhh
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNA--KPGRESTDIEIYGMQ----GIPPDVLAAHYGEE 98 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~--~~grr~~~C~~Cgk~----F~~~s~L~~H~r~h 98 (315)
.-||+|.+|++.|.+. +++.-+.|-|..| ...++.-.|-+|++. |.....|.+-+..+
T Consensus 239 ~~Pf~c~icr~~f~~p--------Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~akeL~~~L~~k 302 (313)
T KOG1813|consen 239 LLPFKCFICRKYFYRP--------VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNVAKELLVSLKLK 302 (313)
T ss_pred cCCccccccccccccc--------hhhcCCceeehhhhccccccCCcceecccccccccchHHHHHHHHHhh
Confidence 4589999999998763 3344445566655 344555678888764 44455555555443
No 136
>PF14353 CpXC: CpXC protein
Probab=40.86 E-value=13 Score=30.74 Aligned_cols=44 Identities=25% Similarity=0.348 Sum_probs=29.3
Q ss_pred ccCcCCcccCChH----------HHHHHhc---CCccccccCcccCCCchhhHhHHh
Q 021252 13 WCYYCDREFDDEK----------ILVQHQK---AKHFKCHVCHKKLSTAGGMAIHVL 56 (315)
Q Consensus 13 ~C~~CgK~F~~~s----------~Lk~H~r---eKPfkC~~CgktF~~~~~L~rH~r 56 (315)
.|..|++.|...- .|+.-+. ---|.|..||+.|.-...+.-|..
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~ 59 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDP 59 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcC
Confidence 5999999885432 2222222 336789999999987777766654
No 137
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.58 E-value=14 Score=31.33 Aligned_cols=12 Identities=25% Similarity=0.617 Sum_probs=6.9
Q ss_pred cccCcCCcccCC
Q 021252 12 VWCYYCDREFDD 23 (315)
Q Consensus 12 ~~C~~CgK~F~~ 23 (315)
++|..||+.|..
T Consensus 71 ~~C~~CG~~~~~ 82 (135)
T PRK03824 71 LKCRNCGNEWSL 82 (135)
T ss_pred EECCCCCCEEec
Confidence 446666666544
No 138
>PRK11823 DNA repair protein RadA; Provisional
Probab=38.31 E-value=21 Score=36.05 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=16.3
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcc
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgk 43 (315)
|.|..||..+. ..-++|..|+.
T Consensus 8 y~C~~Cg~~~~----------~~~g~Cp~C~~ 29 (446)
T PRK11823 8 YVCQECGAESP----------KWLGRCPECGA 29 (446)
T ss_pred EECCcCCCCCc----------ccCeeCcCCCC
Confidence 78999997652 34578998864
No 139
>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=38.11 E-value=20 Score=21.83 Aligned_cols=9 Identities=22% Similarity=0.578 Sum_probs=5.1
Q ss_pred ccccCcccC
Q 021252 37 KCHVCHKKL 45 (315)
Q Consensus 37 kC~~CgktF 45 (315)
.|..||..|
T Consensus 16 ~Cp~CG~~F 24 (26)
T PF10571_consen 16 FCPHCGYDF 24 (26)
T ss_pred cCCCCCCCC
Confidence 455565555
No 140
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=37.39 E-value=7.8 Score=31.38 Aligned_cols=15 Identities=27% Similarity=0.645 Sum_probs=9.7
Q ss_pred CCccccccCcccCCC
Q 021252 33 AKHFKCHVCHKKLST 47 (315)
Q Consensus 33 eKPfkC~~CgktF~~ 47 (315)
+|-|.|..|+.--..
T Consensus 20 ~k~FtCp~Cghe~vs 34 (104)
T COG4888 20 PKTFTCPRCGHEKVS 34 (104)
T ss_pred CceEecCccCCeeee
Confidence 667777777655444
No 141
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=37.23 E-value=18 Score=36.56 Aligned_cols=29 Identities=31% Similarity=0.408 Sum_probs=19.1
Q ss_pred CCCCCCCCCCccccCcCCcccCChHHHHHHhcCCccccccCcc
Q 021252 1 MGKKKKRVSSKVWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (315)
Q Consensus 1 m~rKk~~~~eK~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgk 43 (315)
|.|+|+ .|.|..||..+.+-. =+|..|+.
T Consensus 1 MaK~~t----~f~C~~CG~~s~KW~----------GkCp~Cg~ 29 (456)
T COG1066 1 MAKKKT----AFVCQECGYVSPKWL----------GKCPACGA 29 (456)
T ss_pred CCCccc----EEEcccCCCCCcccc----------ccCCCCCC
Confidence 566663 377999997764332 26888873
No 142
>PF15168 TRIQK: Triple QxxK/R motif-containing protein family
Probab=36.76 E-value=8.7 Score=29.49 Aligned_cols=22 Identities=32% Similarity=0.520 Sum_probs=16.2
Q ss_pred HHHHHHHHHhcCceEEEeeecc
Q 021252 293 FLFTMLCLIEKGVSFFFFNFSY 314 (315)
Q Consensus 293 ~~~~~~~~~~~~~~~~~~~~~~ 314 (315)
+|-.+|||+-....|||.||+-
T Consensus 54 ~l~ail~lL~a~Ya~fyl~ls~ 75 (79)
T PF15168_consen 54 VLAAILVLLLAFYAFFYLNLSK 75 (79)
T ss_pred HHHHHHHHHHHHHHHHHHhhcc
Confidence 3556677777777889988874
No 143
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.71 E-value=12 Score=31.59 Aligned_cols=36 Identities=19% Similarity=0.444 Sum_probs=20.6
Q ss_pred ccccCcCCcccCChHHHHHHhc-CCccccccCcccCCCc
Q 021252 11 KVWCYYCDREFDDEKILVQHQK-AKHFKCHVCHKKLSTA 48 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r-eKPfkC~~CgktF~~~ 48 (315)
+.+|..|+... ...+..+.+ ...|+|..|+++|...
T Consensus 30 ~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 30 KVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cCcCCCCCccc--eeeECCccccccccccCCcCcceeee
Confidence 34577777543 111111222 5568888888888754
No 144
>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=36.36 E-value=23 Score=35.93 Aligned_cols=23 Identities=30% Similarity=0.600 Sum_probs=16.9
Q ss_pred ccccCcCCcccCChHHHHHHhcCCccccccCcc
Q 021252 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHK 43 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~reKPfkC~~Cgk 43 (315)
.|.|..||..+. ..-++|..|+.
T Consensus 7 ~y~C~~Cg~~~~----------~~~g~Cp~C~~ 29 (454)
T TIGR00416 7 KFVCQHCGADSP----------KWQGKCPACHA 29 (454)
T ss_pred eEECCcCCCCCc----------cccEECcCCCC
Confidence 378999997652 34578999964
No 145
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=36.31 E-value=15 Score=32.20 Aligned_cols=9 Identities=44% Similarity=1.412 Sum_probs=6.5
Q ss_pred ccccCcCCc
Q 021252 11 KVWCYYCDR 19 (315)
Q Consensus 11 K~~C~~CgK 19 (315)
||+|++|+.
T Consensus 3 RYyCDYCdt 11 (165)
T KOG3454|consen 3 RYYCDYCDT 11 (165)
T ss_pred cchhhhhhh
Confidence 577888873
No 146
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=36.27 E-value=18 Score=32.16 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=20.0
Q ss_pred ccccCcCCcccCChHHHHHHhc
Q 021252 11 KVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r 32 (315)
-|+|++|+-+|.+.-++..|+.
T Consensus 75 GyyCdVCdcvvKDSinflDHiN 96 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHIN 96 (193)
T ss_pred ceeeeecceeehhhHHHHHHhc
Confidence 4789999999999999998887
No 147
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=35.79 E-value=58 Score=31.90 Aligned_cols=79 Identities=11% Similarity=0.074 Sum_probs=50.8
Q ss_pred ccccCcCCcccCChHHHHHHhcCCccccccCcccCCCchhhHhHHhhhcc-----Cc----------ccccCCCCCCCCc
Q 021252 11 KVWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAIHVLQVHK-----EN----------VTKVPNAKPGRES 75 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~~~L~rH~r~hh~-----ek----------p~~cp~~~~grr~ 75 (315)
-|.|..|..... +-|-+|..|+-++...-+|.|-.+.--. |. .|.|..-......
T Consensus 276 Gy~CP~CkakvC----------sLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~ 345 (378)
T KOG2807|consen 276 GYFCPQCKAKVC----------SLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGR 345 (378)
T ss_pred ceeCCcccCeee----------cCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCc
Confidence 356777763211 6788999999999999999876421111 11 2333211222334
Q ss_pred cccccCCCCCCCHHHHHHHHhhhc
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
|+|+.|...|.-.-+.-.|...|.
T Consensus 346 y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 346 YRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred EEchhccceeeccchHHHHhhhhc
Confidence 999999999988877778877664
No 148
>COG1773 Rubredoxin [Energy production and conversion]
Probab=35.26 E-value=14 Score=26.65 Aligned_cols=13 Identities=23% Similarity=0.616 Sum_probs=7.3
Q ss_pred ccccCcCCcccCC
Q 021252 11 KVWCYYCDREFDD 23 (315)
Q Consensus 11 K~~C~~CgK~F~~ 23 (315)
+|+|..||..|.-
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 3556666666543
No 149
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=35.18 E-value=14 Score=30.26 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=12.6
Q ss_pred cccccCcccCCCchhhHhHHh
Q 021252 36 FKCHVCHKKLSTAGGMAIHVL 56 (315)
Q Consensus 36 fkC~~CgktF~~~~~L~rH~r 56 (315)
|-|-+|.+-|.+...|..|.+
T Consensus 56 hYCieCaryf~t~~aL~~Hkk 76 (126)
T COG5112 56 HYCIECARYFITEKALMEHKK 76 (126)
T ss_pred eeeehhHHHHHHHHHHHHHhc
Confidence 456666666666666666553
No 150
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=35.07 E-value=21 Score=34.63 Aligned_cols=25 Identities=8% Similarity=-0.223 Sum_probs=21.3
Q ss_pred ccccccCCCCCCCHHHHHHHHhhhc
Q 021252 75 STDIEIYGMQGIPPDVLAAHYGEEE 99 (315)
Q Consensus 75 ~~~C~~Cgk~F~~~s~L~~H~r~h~ 99 (315)
+|+|+.|...|.-..+.-.|...|.
T Consensus 388 rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 388 RYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ceechhhhhhhhhhhHHHHHHHHhh
Confidence 3999999999998888888887764
No 151
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.38 E-value=23 Score=29.22 Aligned_cols=16 Identities=19% Similarity=0.312 Sum_probs=10.0
Q ss_pred cCcCCcccCChHHHHH
Q 021252 14 CYYCDREFDDEKILVQ 29 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~ 29 (315)
|..||-......+|.|
T Consensus 18 CpiCgLtLVss~HLAR 33 (112)
T TIGR00622 18 CPICGLTLILSTHLAR 33 (112)
T ss_pred CCcCCCEEeccchHHH
Confidence 6666666666666655
No 152
>PHA00626 hypothetical protein
Probab=32.74 E-value=33 Score=24.97 Aligned_cols=16 Identities=6% Similarity=-0.126 Sum_probs=12.7
Q ss_pred CccccccCCCCCCCHH
Q 021252 74 ESTDIEIYGMQGIPPD 89 (315)
Q Consensus 74 r~~~C~~Cgk~F~~~s 89 (315)
..|.|..||..|....
T Consensus 22 nrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 22 DDYVCCDCGYNDSKDA 37 (59)
T ss_pred cceEcCCCCCeechhh
Confidence 4599999999987653
No 153
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=32.01 E-value=24 Score=36.01 Aligned_cols=24 Identities=29% Similarity=0.765 Sum_probs=20.3
Q ss_pred CCccccCcCCcccCChHHHHHHhc
Q 021252 9 SSKVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 9 ~eK~~C~~CgK~F~~~s~Lk~H~r 32 (315)
++-++|-.|+|.|.....|+.|..
T Consensus 290 ge~lyC~vCnKsFKseKq~kNHEn 313 (508)
T KOG0717|consen 290 GEVLYCVVCNKSFKSEKQLKNHEN 313 (508)
T ss_pred CCceEEeeccccccchHHHHhhHH
Confidence 444789999999999999999977
No 154
>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=31.59 E-value=26 Score=29.71 Aligned_cols=19 Identities=21% Similarity=0.616 Sum_probs=10.3
Q ss_pred ccccCcCCcccCChHHHHHHhc
Q 021252 11 KVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r 32 (315)
...|-+|||.|+.. ++|.+
T Consensus 72 ~i~clecGk~~k~L---krHL~ 90 (132)
T PF05443_consen 72 YIICLECGKKFKTL---KRHLR 90 (132)
T ss_dssp -EE-TBT--EESBH---HHHHH
T ss_pred eeEEccCCcccchH---HHHHH
Confidence 34599999999764 55554
No 155
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=31.58 E-value=16 Score=28.68 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=6.5
Q ss_pred ccccccCccc
Q 021252 35 HFKCHVCHKK 44 (315)
Q Consensus 35 PfkC~~Cgkt 44 (315)
.|.|+.|||.
T Consensus 36 ky~CsfCGK~ 45 (92)
T KOG0402|consen 36 KYTCSFCGKK 45 (92)
T ss_pred hhhhhhcchh
Confidence 4677777654
No 156
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=31.30 E-value=35 Score=25.10 Aligned_cols=33 Identities=24% Similarity=0.404 Sum_probs=20.5
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcccCCCchh
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGG 50 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~~~ 50 (315)
..|.-||+...-.+. .-.|.|..||+.-..+..
T Consensus 10 ~~CtSCg~~i~p~e~------~v~F~CPnCGe~~I~Rc~ 42 (61)
T COG2888 10 PVCTSCGREIAPGET------AVKFPCPNCGEVEIYRCA 42 (61)
T ss_pred ceeccCCCEeccCCc------eeEeeCCCCCceeeehhh
Confidence 358888876532221 456889999866554433
No 157
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.62 E-value=22 Score=29.15 Aligned_cols=10 Identities=30% Similarity=1.291 Sum_probs=5.3
Q ss_pred cccCcCCccc
Q 021252 12 VWCYYCDREF 21 (315)
Q Consensus 12 ~~C~~CgK~F 21 (315)
.+|..||+.|
T Consensus 71 ~~C~~Cg~~~ 80 (113)
T PRK12380 71 AWCWDCSQVV 80 (113)
T ss_pred EEcccCCCEE
Confidence 3455555554
No 158
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.28 E-value=14 Score=39.63 Aligned_cols=52 Identities=21% Similarity=0.441 Sum_probs=29.8
Q ss_pred cCcCCcccCChHHHHHHh---cCCcc-ccccCcccCCCchhhHhHHhhhccCcccccCCCCC
Q 021252 14 CYYCDREFDDEKILVQHQ---KAKHF-KCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKP 71 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~H~---reKPf-kC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~ 71 (315)
|..||-+|+-...|=--+ ..+.| .|+.|.+.|....+-+-| .+ +..|+.|.+
T Consensus 126 CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP~nRRfH-----AQ-p~aCp~CGP 181 (750)
T COG0068 126 CTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDPLNRRFH-----AQ-PIACPKCGP 181 (750)
T ss_pred cCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCccccccc-----cc-cccCcccCC
Confidence 888888877655542111 13444 388887777766654433 32 446666643
No 159
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=30.15 E-value=45 Score=22.32 Aligned_cols=24 Identities=21% Similarity=0.140 Sum_probs=17.4
Q ss_pred cccccCCCCCC--CHHHHHHHHhhhc
Q 021252 76 TDIEIYGMQGI--PPDVLAAHYGEEE 99 (315)
Q Consensus 76 ~~C~~Cgk~F~--~~s~L~~H~r~h~ 99 (315)
..|..||+.+. ..++-+.|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 57889998875 4566678877765
No 160
>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=29.81 E-value=19 Score=25.56 Aligned_cols=17 Identities=29% Similarity=0.841 Sum_probs=10.4
Q ss_pred CCccccCcCCcccCChH
Q 021252 9 SSKVWCYYCDREFDDEK 25 (315)
Q Consensus 9 ~eK~~C~~CgK~F~~~s 25 (315)
..++.|.||++.|....
T Consensus 33 ~~~~rC~YCe~~~~~~e 49 (52)
T PF02748_consen 33 PIKLRCHYCERIITEDE 49 (52)
T ss_dssp TCEEEETTT--EEEHHH
T ss_pred CCEEEeeCCCCEecccE
Confidence 34567999998886554
No 161
>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=29.11 E-value=35 Score=20.48 Aligned_cols=8 Identities=38% Similarity=0.982 Sum_probs=3.9
Q ss_pred ccccccCc
Q 021252 35 HFKCHVCH 42 (315)
Q Consensus 35 PfkC~~Cg 42 (315)
.|.|..||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 45555554
No 162
>PF15269 zf-C2H2_7: Zinc-finger
Probab=28.71 E-value=35 Score=23.75 Aligned_cols=22 Identities=27% Similarity=0.564 Sum_probs=14.6
Q ss_pred ccccCcCCcccCChHHHHHHhc
Q 021252 11 KVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r 32 (315)
+|+|-.|..+...+++|-.|++
T Consensus 20 ~ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 20 KYKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred cceeecCCcccchHHHHHHHHH
Confidence 4457777766666777776665
No 163
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.51 E-value=28 Score=28.57 Aligned_cols=10 Identities=30% Similarity=1.079 Sum_probs=5.0
Q ss_pred cccCcCCccc
Q 021252 12 VWCYYCDREF 21 (315)
Q Consensus 12 ~~C~~CgK~F 21 (315)
.+|..|++.|
T Consensus 71 ~~C~~Cg~~~ 80 (114)
T PRK03681 71 CWCETCQQYV 80 (114)
T ss_pred EEcccCCCee
Confidence 3455555444
No 164
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=28.32 E-value=11 Score=40.27 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=21.9
Q ss_pred ccccccCcccCCCchhhHhHHhhhcc
Q 021252 35 HFKCHVCHKKLSTAGGMAIHVLQVHK 60 (315)
Q Consensus 35 PfkC~~CgktF~~~~~L~rH~r~hh~ 60 (315)
-|-|.+|+|.|.....+..|+++|.-
T Consensus 792 iFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred eeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 48899999999888888888887754
No 165
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=28.25 E-value=16 Score=26.23 Aligned_cols=28 Identities=21% Similarity=0.487 Sum_probs=16.8
Q ss_pred cccCcCCcccCChHHHHHHhcCCccccccCcccCCC
Q 021252 12 VWCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLST 47 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~ 47 (315)
..|..||+.|....+ --.|..|+.-+.|
T Consensus 6 ~~C~~Cg~~~~~~dD--------iVvCp~CgapyHR 33 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDD--------IVVCPECGAPYHR 33 (54)
T ss_pred ccChhhCCcccCCCC--------EEECCCCCCcccH
Confidence 358888887754443 2367777655443
No 166
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=28.20 E-value=1.5e+02 Score=28.79 Aligned_cols=7 Identities=43% Similarity=0.477 Sum_probs=4.2
Q ss_pred ccccCCC
Q 021252 63 VTKVPNA 69 (315)
Q Consensus 63 p~~cp~~ 69 (315)
-|+|++|
T Consensus 310 Df~CpnC 316 (427)
T COG5222 310 DFKCPNC 316 (427)
T ss_pred cccCCCc
Confidence 3566666
No 167
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=28.17 E-value=19 Score=25.30 Aligned_cols=32 Identities=22% Similarity=0.585 Sum_probs=13.3
Q ss_pred cCc--CCcccCChHHHHHHhc----CCcccccc----CcccCC
Q 021252 14 CYY--CDREFDDEKILVQHQK----AKHFKCHV----CHKKLS 46 (315)
Q Consensus 14 C~~--CgK~F~~~s~Lk~H~r----eKPfkC~~----CgktF~ 46 (315)
|.. |.+.+. +..|..|.. .+...|.+ |...+.
T Consensus 12 C~~~cc~~~i~-r~~l~~H~~~~C~~~~v~C~~~~~GC~~~~~ 53 (60)
T PF02176_consen 12 CPNGCCNEMIP-RKELDDHLENECPKRPVPCPYSPYGCKERVP 53 (60)
T ss_dssp -TT--S-BEEE-CCCHHHHHHTTSTTSEEE-SS----S--EEE
T ss_pred CCCCCccccee-HHHHHHHHHccCCCCcEECCCCCCCCCCccc
Confidence 555 333343 334566655 44555665 554443
No 168
>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=27.82 E-value=41 Score=20.27 Aligned_cols=18 Identities=22% Similarity=0.680 Sum_probs=11.2
Q ss_pred ccccCcccCCCchhhHhHH
Q 021252 37 KCHVCHKKLSTAGGMAIHV 55 (315)
Q Consensus 37 kC~~CgktF~~~~~L~rH~ 55 (315)
.|.+|++.+ ....+.+|.
T Consensus 3 ~CPiC~~~v-~~~~in~HL 20 (26)
T smart00734 3 QCPVCFREV-PENLINSHL 20 (26)
T ss_pred cCCCCcCcc-cHHHHHHHH
Confidence 467777666 445666665
No 169
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=27.71 E-value=25 Score=34.73 Aligned_cols=23 Identities=39% Similarity=0.826 Sum_probs=19.8
Q ss_pred CccccCcCCcccCChHHHHHHhc
Q 021252 10 SKVWCYYCDREFDDEKILVQHQK 32 (315)
Q Consensus 10 eK~~C~~CgK~F~~~s~Lk~H~r 32 (315)
++++|..|+|.|.+...+..|..
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~ 259 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLE 259 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHh
Confidence 46789999999999988888866
No 170
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=27.43 E-value=30 Score=29.63 Aligned_cols=26 Identities=15% Similarity=-0.066 Sum_probs=20.5
Q ss_pred cccccCCCCCCCHHHHHHHHhhhcCCCCc
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEEEEVPS 104 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~~e~p~ 104 (315)
.-|-.|||.|. .|++|+.+|.+..+.
T Consensus 77 IicLEDGkkfK---SLKRHL~t~~gmTPd 102 (148)
T COG4957 77 IICLEDGKKFK---SLKRHLTTHYGLTPD 102 (148)
T ss_pred EEEeccCcchH---HHHHHHhcccCCCHH
Confidence 45778888886 699999999887654
No 171
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=27.08 E-value=32 Score=20.20 Aligned_cols=7 Identities=43% Similarity=1.027 Sum_probs=3.2
Q ss_pred cCcCCcc
Q 021252 14 CYYCDRE 20 (315)
Q Consensus 14 C~~CgK~ 20 (315)
|..||+.
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 4444443
No 172
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=26.95 E-value=41 Score=22.28 Aligned_cols=13 Identities=31% Similarity=0.736 Sum_probs=9.3
Q ss_pred ccccccCcccCCC
Q 021252 35 HFKCHVCHKKLST 47 (315)
Q Consensus 35 PfkC~~CgktF~~ 47 (315)
+|+|..|++.|-.
T Consensus 12 ~f~C~~C~~~FC~ 24 (39)
T smart00154 12 GFKCRHCGNLFCG 24 (39)
T ss_pred CeECCccCCcccc
Confidence 6777777777765
No 173
>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=26.89 E-value=43 Score=23.20 Aligned_cols=26 Identities=19% Similarity=0.659 Sum_probs=17.5
Q ss_pred cCcCCcccCChHHHHHHhcCCccccccCcccCCC
Q 021252 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLST 47 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~ 47 (315)
|..|++.|... .+.+.|..||+.|-.
T Consensus 5 C~~C~~~F~~~--------~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 5 CMGCGKPFTLT--------RRRHHCRNCGRIFCS 30 (57)
T ss_pred CcccCccccCC--------ccccccCcCcCCcCh
Confidence 77788877641 445677777777665
No 174
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=26.47 E-value=19 Score=35.69 Aligned_cols=17 Identities=24% Similarity=0.341 Sum_probs=8.5
Q ss_pred cccCcccCCCchhhHhHH
Q 021252 38 CHVCHKKLSTAGGMAIHV 55 (315)
Q Consensus 38 C~~CgktF~~~~~L~rH~ 55 (315)
|+-| |.|.+++-+++|+
T Consensus 39 CdGC-KGFFRRSVrk~~~ 55 (432)
T KOG4215|consen 39 CDGC-KGFFRRSVRKNHQ 55 (432)
T ss_pred cCcc-hHHHHHHHHhcce
Confidence 5555 4455555555554
No 175
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=26.14 E-value=57 Score=29.33 Aligned_cols=29 Identities=24% Similarity=0.254 Sum_probs=21.8
Q ss_pred hhHHHHHHHHHHHHHHHHhcCceEEEeee
Q 021252 284 IILSLIMKIFLFTMLCLIEKGVSFFFFNF 312 (315)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 312 (315)
-..-.|||-||+|+.-+-+.=+..||+|=
T Consensus 101 ~LG~~Lm~~f~~~L~e~~~~p~~Ifl~n~ 129 (194)
T TIGR03527 101 ELGRILMKGFIYTLSELDPLPKRILFVNG 129 (194)
T ss_pred HHHHHHHHHHHHHHHhCCCCceEEEEEcc
Confidence 46788999999998765444477888873
No 176
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.87 E-value=34 Score=28.18 Aligned_cols=9 Identities=33% Similarity=0.741 Sum_probs=4.9
Q ss_pred ccCcCCccc
Q 021252 13 WCYYCDREF 21 (315)
Q Consensus 13 ~C~~CgK~F 21 (315)
+|..||+.|
T Consensus 73 ~C~~Cg~~~ 81 (117)
T PRK00564 73 ECKDCSHVF 81 (117)
T ss_pred EhhhCCCcc
Confidence 455555554
No 177
>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=25.68 E-value=28 Score=25.35 Aligned_cols=28 Identities=18% Similarity=0.605 Sum_probs=12.4
Q ss_pred ccCcCCcccCChHHHHHHhcCCccccccCcccCCCc
Q 021252 13 WCYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTA 48 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~ 48 (315)
.|..|++.|... .|.+.|..||+.|-..
T Consensus 11 ~C~~C~~~F~~~--------~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 11 NCMICGKKFSLF--------RRRHHCRNCGRVVCSS 38 (69)
T ss_dssp B-TTT--B-BSS--------S-EEE-TTT--EEECC
T ss_pred cCcCcCCcCCCc--------eeeEccCCCCCEECCc
Confidence 488888888431 4566777777766543
No 178
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=25.39 E-value=33 Score=29.08 Aligned_cols=13 Identities=38% Similarity=0.843 Sum_probs=7.0
Q ss_pred ccCcCCcccCChH
Q 021252 13 WCYYCDREFDDEK 25 (315)
Q Consensus 13 ~C~~CgK~F~~~s 25 (315)
+|..||+.|.+.+
T Consensus 3 ~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 3 QCTKCGRVFEDGS 15 (131)
T ss_pred ccCcCCCCcCCCc
Confidence 3555666655443
No 179
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=25.32 E-value=34 Score=35.83 Aligned_cols=27 Identities=7% Similarity=0.037 Sum_probs=21.6
Q ss_pred cccccCCCCCCCHHHHHHHHhhhcCCC
Q 021252 76 TDIEIYGMQGIPPDVLAAHYGEEEEEV 102 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r~h~~e~ 102 (315)
-+|..||++|.+....++||..|.++.
T Consensus 419 nqC~~CG~R~~~~ee~sk~md~H~dwh 445 (579)
T KOG2071|consen 419 NQCKSCGLRFDDSEERSKHMDIHDDWH 445 (579)
T ss_pred chhcccccccccchhhhhHhhhhhhhh
Confidence 678899999988888888888776543
No 180
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.81 E-value=44 Score=23.61 Aligned_cols=14 Identities=36% Similarity=0.643 Sum_probs=10.6
Q ss_pred cCcCCcccCChHHH
Q 021252 14 CYYCDREFDDEKIL 27 (315)
Q Consensus 14 C~~CgK~F~~~s~L 27 (315)
|..|++.|.....-
T Consensus 15 CpvCqRPFsWRkKW 28 (54)
T COG4338 15 CPVCQRPFSWRKKW 28 (54)
T ss_pred hhhhcCchHHHHHH
Confidence 99999998765543
No 181
>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=24.60 E-value=50 Score=33.94 Aligned_cols=44 Identities=18% Similarity=0.287 Sum_probs=0.0
Q ss_pred cCcCCcccCChHHHHHHhcCCccccccCcccCCCchhhHhHHhhhccCcccccCCCCCCCC-ccccccCC
Q 021252 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAIHVLQVHKENVTKVPNAKPGRE-STDIEIYG 82 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~~~L~rH~r~hh~ekp~~cp~~~~grr-~~~C~~Cg 82 (315)
|..||... +|..|+-.+. .|..+....|..|..... ...|..|+
T Consensus 216 C~~Cg~~~---------------~C~~C~~~l~----------~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~ 260 (505)
T TIGR00595 216 CRSCGYIL---------------CCPNCDVSLT----------YHKKEGKLRCHYCGYQEPIPKTCPQCG 260 (505)
T ss_pred hhhCcCcc---------------CCCCCCCceE----------EecCCCeEEcCCCcCcCCCCCCCCCCC
No 182
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.55 E-value=32 Score=34.68 Aligned_cols=36 Identities=19% Similarity=0.490 Sum_probs=23.8
Q ss_pred ccccCcCCcccCChHHHHHHhc-CCccccccCcccCC
Q 021252 11 KVWCYYCDREFDDEKILVQHQK-AKHFKCHVCHKKLS 46 (315)
Q Consensus 11 K~~C~~CgK~F~~~s~Lk~H~r-eKPfkC~~CgktF~ 46 (315)
-|.|..|.|.|.....++.-.- +--|.|..|+.-..
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 4568888888877766654433 55688888865443
No 183
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=24.43 E-value=41 Score=24.14 Aligned_cols=19 Identities=32% Similarity=0.973 Sum_probs=16.1
Q ss_pred cccCcCCcccCChHHHHHH
Q 021252 12 VWCYYCDREFDDEKILVQH 30 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H 30 (315)
++|-+||..|.+...|.++
T Consensus 28 ~YC~~Cg~~Y~d~~dL~~~ 46 (55)
T PF13821_consen 28 NYCFWCGTKYDDEEDLERN 46 (55)
T ss_pred ceeeeeCCccCCHHHHHhC
Confidence 4699999999999888754
No 184
>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=24.21 E-value=34 Score=28.07 Aligned_cols=11 Identities=27% Similarity=0.821 Sum_probs=5.0
Q ss_pred cccccCcccCC
Q 021252 36 FKCHVCHKKLS 46 (315)
Q Consensus 36 fkC~~CgktF~ 46 (315)
++|..|++.|.
T Consensus 71 ~~C~~Cg~~~~ 81 (115)
T TIGR00100 71 CECEDCSEEVS 81 (115)
T ss_pred EEcccCCCEEe
Confidence 44544544443
No 185
>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=23.94 E-value=22 Score=25.28 Aligned_cols=42 Identities=19% Similarity=0.525 Sum_probs=18.2
Q ss_pred cCcCCcccCChHHHHHHhcCCccccccCcccCCCchhhHhHHhh
Q 021252 14 CYYCDREFDDEKILVQHQKAKHFKCHVCHKKLSTAGGMAIHVLQ 57 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~H~reKPfkC~~CgktF~~~~~L~rH~r~ 57 (315)
|--|.+.|.....-..- ...|+|..|++.|--.-++-.|+..
T Consensus 2 CfgC~~~~~~~~~~~~~--~~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKAD--SSRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp ETTTTEE-TTS---------EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CccCCCCCCCccccccc--CCeEECCCCCCccccCcChhhhccc
Confidence 44466666554321100 3467777777777777776666543
No 186
>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 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=23.60 E-value=47 Score=28.20 Aligned_cols=22 Identities=5% Similarity=-0.390 Sum_probs=16.5
Q ss_pred ccccccCCCCCCCHHHHHHHHh
Q 021252 75 STDIEIYGMQGIPPDVLAAHYG 96 (315)
Q Consensus 75 ~~~C~~Cgk~F~~~s~L~~H~r 96 (315)
=+.|..||+-|-..+..++..+
T Consensus 124 f~~C~~C~kiyW~GsH~~~~~~ 145 (147)
T PF01927_consen 124 FWRCPGCGKIYWEGSHWRRMEE 145 (147)
T ss_pred EEECCCCCCEecccccHHHHHh
Confidence 4888899998877777666544
No 188
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=23.25 E-value=61 Score=28.10 Aligned_cols=30 Identities=27% Similarity=0.616 Sum_probs=15.4
Q ss_pred ccCcCCcccCChHHHHHHhc-CCccccccCcc
Q 021252 13 WCYYCDREFDDEKILVQHQK-AKHFKCHVCHK 43 (315)
Q Consensus 13 ~C~~CgK~F~~~s~Lk~H~r-eKPfkC~~Cgk 43 (315)
+|..|++.+....... ... +..-+|..|+.
T Consensus 107 ~C~~C~~~~~~~~~~~-~~~~~~~~~C~~C~~ 137 (178)
T PF02146_consen 107 RCSKCGKEYDREDIVD-SIDEEEPPRCPKCGG 137 (178)
T ss_dssp EETTTSBEEEGHHHHH-HHHTTSSCBCTTTSC
T ss_pred eecCCCccccchhhcc-cccccccccccccCc
Confidence 4777777665443322 222 33346666665
No 189
>PRK14873 primosome assembly protein PriA; Provisional
Probab=23.20 E-value=50 Score=35.34 Aligned_cols=31 Identities=16% Similarity=0.253 Sum_probs=19.2
Q ss_pred ccCcCCcccCCh---HHHHHHhcCCccccccCcc
Q 021252 13 WCYYCDREFDDE---KILVQHQKAKHFKCHVCHK 43 (315)
Q Consensus 13 ~C~~CgK~F~~~---s~Lk~H~reKPfkC~~Cgk 43 (315)
.|..||..+... ..|.-|...+..+|+.||.
T Consensus 385 ~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 385 ACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred EhhhCcCeeECCCCCCceeEecCCCeeECCCCcC
Confidence 377777776533 3456665555667777763
No 190
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=22.67 E-value=63 Score=32.90 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=27.2
Q ss_pred CCccccccCc-ccCCCchhhHhHHh---hhccCcccccCCC
Q 021252 33 AKHFKCHVCH-KKLSTAGGMAIHVL---QVHKENVTKVPNA 69 (315)
Q Consensus 33 eKPfkC~~Cg-ktF~~~~~L~rH~r---~hh~ekp~~cp~~ 69 (315)
.+-|.|.+|| +++..+..+.||.. ..||-+.+..+++
T Consensus 399 ~~ey~CEICGNy~Y~GrkaF~RHF~EwRH~hGmrCLGIpnt 439 (497)
T KOG2636|consen 399 DIEYNCEICGNYVYKGRKAFDRHFNEWRHAHGMRCLGIPNT 439 (497)
T ss_pred CcccceeeccCccccCcHHHHHHhHHHHHhhcceecCCCCc
Confidence 7788999998 78888888888863 3356665555554
No 191
>KOG3815 consensus Transcription factor Doublesex [Transcription]
Probab=22.59 E-value=37 Score=32.85 Aligned_cols=44 Identities=18% Similarity=0.265 Sum_probs=31.1
Q ss_pred CCccccCcCCcccCChHHHHHHhc---CCccccccCcccCCCchhhHh
Q 021252 9 SSKVWCYYCDREFDDEKILVQHQK---AKHFKCHVCHKKLSTAGGMAI 53 (315)
Q Consensus 9 ~eK~~C~~CgK~F~~~s~Lk~H~r---eKPfkC~~CgktF~~~~~L~r 53 (315)
..++||..|. -+.....||.|.| .|.-.|.+|.....++..+..
T Consensus 34 ~r~p~CaRCr-nHG~~~~LKGHk~~C~~~~C~C~kC~li~eRqrvmaa 80 (322)
T KOG3815|consen 34 ARGPKCARCE-NHGVLSRLKGHKRSCPYRDCPCEKCGLVEERRRVMAA 80 (322)
T ss_pred cccchhhhhh-ccCcceeccCCCCCCCCCCCCchHhcchHHHHHHHHH
Confidence 3467888885 3556778899988 666778888877776655443
No 192
>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=22.44 E-value=79 Score=21.60 Aligned_cols=15 Identities=33% Similarity=0.574 Sum_probs=10.9
Q ss_pred cCcCCcccCChHHHH
Q 021252 14 CYYCDREFDDEKILV 28 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk 28 (315)
|.+|++.|.......
T Consensus 11 C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 11 CPVCGRPFTWRKKWA 25 (42)
T ss_pred CcccCCcchHHHHHH
Confidence 888888887665443
No 193
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=22.20 E-value=7.6e+02 Score=24.28 Aligned_cols=28 Identities=18% Similarity=0.433 Sum_probs=22.6
Q ss_pred CCcccccc---CcccCCCchhhHhHHhhhcc
Q 021252 33 AKHFKCHV---CHKKLSTAGGMAIHVLQVHK 60 (315)
Q Consensus 33 eKPfkC~~---CgktF~~~~~L~rH~r~hh~ 60 (315)
+--|.|.. |.++|..+.+|..|+...|+
T Consensus 142 g~iFmC~~~~GC~RTyLsqrDlqAHInhrH~ 172 (389)
T KOG2932|consen 142 GGIFMCAAPHGCLRTYLSQRDLQAHINHRHG 172 (389)
T ss_pred cceEEeecchhHHHHHhhHHHHHHHhhhhhc
Confidence 55677764 99999999999999866665
No 194
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=21.57 E-value=23 Score=24.46 Aligned_cols=36 Identities=28% Similarity=0.655 Sum_probs=20.6
Q ss_pred cCcCCcccCChHHHHHHh-c---CCccccccCcccCCCch
Q 021252 14 CYYCDREFDDEKILVQHQ-K---AKHFKCHVCHKKLSTAG 49 (315)
Q Consensus 14 C~~CgK~F~~~s~Lk~H~-r---eKPfkC~~CgktF~~~~ 49 (315)
|..|++..........-. + ..-|+|..|++.+....
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSS
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCe
Confidence 556666665333221111 1 66788888888776554
No 195
>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=21.09 E-value=50 Score=23.97 Aligned_cols=14 Identities=21% Similarity=0.662 Sum_probs=8.3
Q ss_pred CCccccccCcccCC
Q 021252 33 AKHFKCHVCHKKLS 46 (315)
Q Consensus 33 eKPfkC~~CgktF~ 46 (315)
.+-|.|..||..+.
T Consensus 44 ~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 44 GRVFTCPNCGFEMD 57 (69)
T ss_pred cceEEcCCCCCEEC
Confidence 55666666665543
No 196
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.83 E-value=77 Score=27.98 Aligned_cols=21 Identities=5% Similarity=-0.278 Sum_probs=10.9
Q ss_pred cccccCCCCCCCHHHHHHHHh
Q 021252 76 TDIEIYGMQGIPPDVLAAHYG 96 (315)
Q Consensus 76 ~~C~~Cgk~F~~~s~L~~H~r 96 (315)
+.|..||+.|-..+..++..+
T Consensus 131 ~~C~~CgkiYW~GsHw~~m~~ 151 (165)
T COG1656 131 YRCPKCGKIYWKGSHWRRMVE 151 (165)
T ss_pred eECCCCcccccCchHHHHHHH
Confidence 555555555555555554444
No 197
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=20.39 E-value=27 Score=25.30 Aligned_cols=32 Identities=19% Similarity=0.567 Sum_probs=16.9
Q ss_pred cccCcCCcccCChHHHHHHh--c---CCccccccCcc
Q 021252 12 VWCYYCDREFDDEKILVQHQ--K---AKHFKCHVCHK 43 (315)
Q Consensus 12 ~~C~~CgK~F~~~s~Lk~H~--r---eKPfkC~~Cgk 43 (315)
.+|-.|||.+.-......-. + ...|-|+.|..
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~ 39 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKE 39 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHH
Confidence 45777777765433222221 2 34477777743
No 198
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=20.11 E-value=57 Score=33.43 Aligned_cols=29 Identities=31% Similarity=0.460 Sum_probs=24.0
Q ss_pred CCccccccCcccCCCchhhHhHHhhhccC
Q 021252 33 AKHFKCHVCHKKLSTAGGMAIHVLQVHKE 61 (315)
Q Consensus 33 eKPfkC~~CgktF~~~~~L~rH~r~hh~e 61 (315)
-+=|.|..|.+.|.....+..|+...|..
T Consensus 55 WrFWiCp~CskkF~d~~~~~~H~~~eH~~ 83 (466)
T PF04780_consen 55 WRFWICPRCSKKFSDAESCLSHMEQEHPA 83 (466)
T ss_pred eeEeeCCcccceeCCHHHHHHHHHHhhhh
Confidence 44578999999999999999999877753
Done!