Query 041528
Match_columns 527
No_of_seqs 137 out of 1551
Neff 9.2
Searched_HMMs 46136
Date Fri Mar 29 08:05:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041528hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1074 Transcriptional repres 100.0 1.9E-31 4.1E-36 273.0 7.6 61 430-492 879-939 (958)
2 KOG1074 Transcriptional repres 99.9 1.3E-23 2.7E-28 216.0 9.8 55 74-128 605-663 (958)
3 KOG3623 Homeobox transcription 99.9 3.2E-22 7E-27 202.0 6.3 82 373-482 891-972 (1007)
4 KOG2462 C2H2-type Zn-finger pr 99.8 1.9E-21 4.1E-26 177.8 3.0 135 346-482 126-265 (279)
5 KOG2462 C2H2-type Zn-finger pr 99.8 2.8E-21 6.1E-26 176.6 2.2 111 373-487 127-242 (279)
6 KOG3608 Zn finger proteins [Ge 99.6 4.6E-17 1E-21 152.4 -3.6 80 374-483 290-376 (467)
7 KOG3576 Ovo and related transc 99.5 3.2E-16 6.9E-21 135.9 -2.5 85 373-485 114-199 (267)
8 KOG3608 Zn finger proteins [Ge 99.5 1.3E-15 2.8E-20 142.8 -2.4 110 376-488 237-349 (467)
9 KOG3623 Homeobox transcription 99.3 1.5E-13 3.2E-18 140.0 0.4 80 8-119 892-971 (1007)
10 KOG3576 Ovo and related transc 99.3 1.7E-13 3.7E-18 119.1 0.3 83 8-122 115-198 (267)
11 PHA00733 hypothetical protein 98.8 7.9E-10 1.7E-14 93.5 0.4 85 373-484 37-123 (128)
12 PHA02768 hypothetical protein; 98.7 2E-09 4.4E-14 74.6 -0.0 44 431-478 6-49 (55)
13 PHA02768 hypothetical protein; 98.7 3E-09 6.4E-14 73.8 0.6 43 376-418 5-47 (55)
14 PF13465 zf-H2C2_2: Zinc-finge 98.6 3.6E-09 7.9E-14 62.7 -1.0 26 447-472 1-26 (26)
15 PLN03086 PRLI-interacting fact 98.6 1.3E-08 2.9E-13 105.5 1.1 101 373-480 450-560 (567)
16 KOG3993 Transcription factor ( 98.5 3.3E-08 7.1E-13 95.9 1.1 113 375-489 355-488 (500)
17 PHA00733 hypothetical protein 98.4 8E-08 1.7E-12 81.3 2.0 82 8-123 38-124 (128)
18 PF13465 zf-H2C2_2: Zinc-finge 98.4 8.1E-08 1.7E-12 56.9 0.8 25 86-110 2-26 (26)
19 PLN03086 PRLI-interacting fact 98.4 2.9E-07 6.4E-12 95.6 5.0 109 7-122 450-565 (567)
20 PHA00732 hypothetical protein 98.3 1.6E-07 3.5E-12 71.8 1.6 25 376-400 1-26 (79)
21 PHA00616 hypothetical protein 98.3 2.3E-07 5E-12 61.2 0.8 34 10-44 1-34 (44)
22 KOG3993 Transcription factor ( 98.1 3E-07 6.4E-12 89.4 -1.7 110 375-485 266-381 (500)
23 PF00096 zf-C2H2: Zinc finger, 98.0 9.3E-07 2E-11 50.8 -0.7 23 461-483 1-23 (23)
24 PHA00616 hypothetical protein 97.9 4.8E-06 1E-10 55.0 1.8 31 98-128 1-31 (44)
25 PF00096 zf-C2H2: Zinc finger, 97.8 9.9E-06 2.1E-10 46.5 1.7 23 99-121 1-23 (23)
26 PF05605 zf-Di19: Drought indu 97.8 4E-06 8.8E-11 59.5 -0.1 51 430-484 2-53 (54)
27 COG5189 SFP1 Putative transcri 97.8 1E-05 2.2E-10 75.9 2.4 66 374-481 347-419 (423)
28 PF13912 zf-C2H2_6: C2H2-type 97.5 2.2E-05 4.7E-10 47.0 0.2 26 460-485 1-26 (27)
29 PF13912 zf-C2H2_6: C2H2-type 97.5 2.5E-05 5.4E-10 46.8 -0.1 26 376-401 1-26 (27)
30 PHA00732 hypothetical protein 97.5 7.4E-05 1.6E-09 57.2 2.4 39 10-52 1-40 (79)
31 PF12756 zf-C2H2_2: C2H2 type 97.5 3.1E-05 6.7E-10 62.9 0.2 73 378-483 1-73 (100)
32 COG5189 SFP1 Putative transcri 97.4 9.5E-05 2E-09 69.6 2.3 70 8-119 347-419 (423)
33 PF13894 zf-C2H2_4: C2H2-type 97.3 0.00012 2.7E-09 42.1 1.9 24 99-122 1-24 (24)
34 PF13894 zf-C2H2_4: C2H2-type 97.2 0.0002 4.3E-09 41.3 1.8 24 11-34 1-24 (24)
35 smart00355 ZnF_C2H2 zinc finge 97.1 0.00017 3.7E-09 42.3 0.7 25 461-485 1-25 (26)
36 PF09237 GAGA: GAGA factor; I 96.8 0.001 2.2E-08 45.0 2.5 34 94-127 20-53 (54)
37 smart00355 ZnF_C2H2 zinc finge 96.7 0.0011 2.3E-08 38.8 1.9 24 99-122 1-24 (26)
38 PF09237 GAGA: GAGA factor; I 96.7 0.0014 3E-08 44.3 2.3 33 6-38 20-52 (54)
39 PF05605 zf-Di19: Drought indu 96.6 0.0015 3.2E-08 46.3 2.2 49 64-122 3-53 (54)
40 PF12171 zf-C2H2_jaz: Zinc-fin 96.5 0.00082 1.8E-08 40.0 0.5 23 377-399 2-24 (27)
41 PF12874 zf-met: Zinc-finger o 96.5 0.00052 1.1E-08 40.1 -0.4 23 461-483 1-23 (25)
42 PF12874 zf-met: Zinc-finger o 96.5 0.00045 9.8E-09 40.3 -0.8 23 377-399 1-23 (25)
43 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.0019 4.1E-08 38.5 1.2 23 461-483 2-24 (27)
44 PF12756 zf-C2H2_2: C2H2 type 96.3 0.0025 5.5E-08 51.5 2.2 73 12-122 1-74 (100)
45 PF13909 zf-H2C2_5: C2H2-type 95.3 0.011 2.4E-07 33.9 1.7 23 99-122 1-23 (24)
46 PRK04860 hypothetical protein; 94.9 0.0079 1.7E-07 52.9 0.3 23 375-401 118-140 (160)
47 PF13909 zf-H2C2_5: C2H2-type 94.8 0.018 3.9E-07 33.0 1.5 24 11-35 1-24 (24)
48 PF13913 zf-C2HC_2: zinc-finge 94.2 0.015 3.4E-07 33.7 0.4 21 461-482 3-23 (25)
49 PRK04860 hypothetical protein; 93.7 0.03 6.4E-07 49.3 1.3 42 70-112 115-157 (160)
50 smart00451 ZnF_U1 U1-like zinc 93.0 0.027 5.8E-07 35.7 -0.1 24 375-398 2-25 (35)
51 smart00451 ZnF_U1 U1-like zinc 92.8 0.04 8.7E-07 34.9 0.5 23 460-482 3-25 (35)
52 PF13913 zf-C2HC_2: zinc-finge 92.2 0.11 2.3E-06 30.2 1.7 21 99-120 3-23 (25)
53 KOG2893 Zn finger protein [Gen 92.1 0.04 8.7E-07 50.1 -0.2 47 433-485 13-60 (341)
54 COG5048 FOG: Zn-finger [Genera 91.7 0.12 2.6E-06 53.7 2.8 58 429-488 288-351 (467)
55 KOG1146 Homeobox protein [Gene 91.4 0.082 1.8E-06 59.9 1.2 79 375-485 464-545 (1406)
56 KOG2231 Predicted E3 ubiquitin 90.8 0.045 9.7E-07 58.4 -1.4 98 379-483 118-235 (669)
57 COG5048 FOG: Zn-finger [Genera 90.6 0.41 9E-06 49.6 5.6 51 436-488 394-446 (467)
58 PF09538 FYDLN_acid: Protein o 89.7 0.31 6.7E-06 39.8 2.9 32 429-473 8-39 (108)
59 PRK14890 putative Zn-ribbon RN 88.4 0.31 6.8E-06 34.5 1.7 34 61-106 23-56 (59)
60 KOG1146 Homeobox protein [Gene 86.1 0.13 2.9E-06 58.3 -1.8 93 374-482 1258-1350(1406)
61 TIGR02300 FYDLN_acid conserved 85.7 0.75 1.6E-05 38.1 2.8 36 429-477 8-43 (129)
62 KOG2231 Predicted E3 ubiquitin 85.0 0.46 1E-05 50.9 1.7 101 18-122 122-236 (669)
63 COG2888 Predicted Zn-ribbon RN 84.6 0.42 9E-06 33.7 0.7 38 57-106 21-58 (61)
64 cd00350 rubredoxin_like Rubred 83.6 0.76 1.6E-05 28.7 1.6 25 431-469 2-26 (33)
65 COG4049 Uncharacterized protei 79.6 0.77 1.7E-05 31.8 0.6 29 4-32 11-39 (65)
66 COG4049 Uncharacterized protei 78.9 0.63 1.4E-05 32.2 -0.0 34 452-485 9-43 (65)
67 smart00614 ZnF_BED BED zinc fi 78.0 0.79 1.7E-05 31.7 0.3 25 461-485 19-49 (50)
68 COG4530 Uncharacterized protei 76.3 1.6 3.4E-05 34.9 1.5 30 431-473 10-39 (129)
69 PF14353 CpXC: CpXC protein 76.1 1.3 2.9E-05 37.5 1.2 23 460-482 38-60 (128)
70 smart00614 ZnF_BED BED zinc fi 75.5 1.9 4.1E-05 29.8 1.7 24 100-123 20-49 (50)
71 PF02892 zf-BED: BED zinc fing 75.2 1.9 4E-05 28.9 1.5 27 95-121 13-44 (45)
72 cd00729 rubredoxin_SM Rubredox 75.0 1.9 4.1E-05 27.1 1.4 23 431-468 3-26 (34)
73 smart00734 ZnF_Rad18 Rad18-lik 74.8 1.3 2.8E-05 26.0 0.5 20 461-481 2-21 (26)
74 PF02892 zf-BED: BED zinc fing 74.1 2.3 5E-05 28.5 1.7 25 7-31 13-41 (45)
75 PF10571 UPF0547: Uncharacteri 72.9 2.8 6E-05 24.6 1.6 14 458-471 12-25 (26)
76 KOG2893 Zn finger protein [Gen 72.8 2.2 4.9E-05 39.1 1.8 40 11-61 11-50 (341)
77 PF05443 ROS_MUCR: ROS/MUCR tr 70.6 2.1 4.6E-05 36.3 1.1 27 9-38 71-97 (132)
78 COG1592 Rubrerythrin [Energy p 70.0 2.8 6.1E-05 37.0 1.8 22 431-467 135-156 (166)
79 KOG4167 Predicted DNA-binding 69.6 0.5 1.1E-05 50.3 -3.4 29 459-487 791-819 (907)
80 PRK00464 nrdR transcriptional 66.7 3.3 7.1E-05 36.2 1.5 21 460-480 28-48 (154)
81 PF09723 Zn-ribbon_8: Zinc rib 65.9 3.9 8.5E-05 27.1 1.4 29 431-468 6-34 (42)
82 PRK00398 rpoP DNA-directed RNA 65.3 3.8 8.1E-05 27.7 1.3 30 430-471 3-32 (46)
83 TIGR02605 CxxC_CxxC_SSSS putat 65.2 3.4 7.3E-05 28.7 1.1 30 376-410 5-34 (52)
84 COG5151 SSL1 RNA polymerase II 65.0 6.2 0.00013 37.9 3.1 49 64-122 363-412 (421)
85 KOG4173 Alpha-SNAP protein [In 64.7 2.1 4.5E-05 38.5 -0.1 78 10-122 79-171 (253)
86 smart00834 CxxC_CXXC_SSSS Puta 64.6 3.6 7.7E-05 26.8 1.1 30 376-410 5-34 (41)
87 TIGR00622 ssl1 transcription f 64.6 14 0.0003 30.3 4.6 26 97-122 80-105 (112)
88 COG5236 Uncharacterized conser 63.6 1.5 3.3E-05 42.5 -1.2 102 377-484 152-276 (493)
89 PHA00626 hypothetical protein 61.1 5.1 0.00011 28.0 1.3 15 98-112 23-37 (59)
90 smart00154 ZnF_AN1 AN1-like Zi 60.2 5.8 0.00013 25.8 1.4 15 460-474 12-26 (39)
91 KOG4167 Predicted DNA-binding 60.1 1.4 3.1E-05 47.0 -2.2 29 373-401 789-817 (907)
92 PF14353 CpXC: CpXC protein 60.0 3.9 8.4E-05 34.6 0.7 23 98-120 38-60 (128)
93 cd00065 FYVE FYVE domain; Zinc 58.4 6.9 0.00015 27.6 1.7 28 432-473 4-31 (57)
94 KOG4124 Putative transcription 58.4 8.4 0.00018 37.7 2.7 71 373-481 346-419 (442)
95 PF05443 ROS_MUCR: ROS/MUCR tr 57.3 3.2 6.9E-05 35.2 -0.2 25 458-485 70-94 (132)
96 COG4957 Predicted transcriptio 56.6 5.5 0.00012 33.3 1.0 25 11-38 77-101 (148)
97 PF09538 FYDLN_acid: Protein o 56.4 7.3 0.00016 31.9 1.7 15 97-111 25-39 (108)
98 COG4957 Predicted transcriptio 55.9 3.5 7.7E-05 34.4 -0.2 24 460-486 76-99 (148)
99 TIGR00622 ssl1 transcription f 55.1 22 0.00047 29.2 4.2 22 374-395 13-34 (112)
100 PF13717 zinc_ribbon_4: zinc-r 54.3 8.7 0.00019 24.4 1.5 32 77-109 5-36 (36)
101 PF03604 DNA_RNApol_7kD: DNA d 52.3 12 0.00027 23.1 1.9 26 431-469 1-26 (32)
102 PRK09678 DNA-binding transcrip 51.7 6.8 0.00015 29.3 0.8 21 456-476 23-45 (72)
103 PF01363 FYVE: FYVE zinc finge 51.6 6.2 0.00013 29.2 0.5 28 431-472 10-37 (69)
104 COG1997 RPL43A Ribosomal prote 50.7 8.1 0.00018 29.8 1.1 32 374-413 33-64 (89)
105 TIGR02098 MJ0042_CXXC MJ0042 f 50.6 9.2 0.0002 24.4 1.2 12 98-109 25-36 (38)
106 KOG1280 Uncharacterized conser 50.4 12 0.00025 36.8 2.3 36 95-130 76-112 (381)
107 PF09986 DUF2225: Uncharacteri 50.2 6.6 0.00014 36.6 0.6 25 8-32 3-27 (214)
108 KOG4173 Alpha-SNAP protein [In 50.2 1.6 3.4E-05 39.3 -3.3 29 457-485 141-172 (253)
109 PF09986 DUF2225: Uncharacteri 49.9 6.6 0.00014 36.6 0.6 25 458-482 3-27 (214)
110 PRK00464 nrdR transcriptional 49.5 7.7 0.00017 34.0 0.9 16 98-113 28-43 (154)
111 smart00659 RPOLCX RNA polymera 48.6 11 0.00024 25.3 1.3 27 431-470 3-29 (44)
112 TIGR00595 priA primosomal prot 47.8 13 0.00029 39.6 2.5 22 431-469 241-262 (505)
113 PF01780 Ribosomal_L37ae: Ribo 47.5 4.9 0.00011 31.4 -0.6 32 429-472 34-65 (90)
114 PF13719 zinc_ribbon_5: zinc-r 47.2 13 0.00028 23.8 1.4 32 77-109 5-36 (37)
115 PRK12496 hypothetical protein; 46.2 11 0.00024 33.4 1.5 27 431-471 128-154 (164)
116 PF12013 DUF3505: Protein of u 46.0 14 0.0003 30.3 1.8 26 98-123 80-109 (109)
117 COG1198 PriA Primosomal protei 45.8 17 0.00036 40.3 2.9 51 375-469 434-484 (730)
118 smart00064 FYVE Protein presen 44.2 15 0.00032 27.0 1.6 28 431-472 11-38 (68)
119 KOG2186 Cell growth-regulating 43.9 7.2 0.00016 36.5 -0.2 49 431-484 4-52 (276)
120 TIGR00373 conserved hypothetic 43.4 7.6 0.00016 34.3 -0.1 31 429-470 108-138 (158)
121 PF05191 ADK_lid: Adenylate ki 43.4 11 0.00024 24.0 0.7 33 431-473 2-34 (36)
122 PRK06266 transcription initiat 43.3 7.8 0.00017 34.9 -0.0 32 429-471 116-147 (178)
123 TIGR02300 FYDLN_acid conserved 43.2 17 0.00036 30.4 1.9 20 96-115 24-43 (129)
124 PF06524 NOA36: NOA36 protein; 43.1 9.5 0.00021 35.8 0.5 89 32-122 136-233 (314)
125 PRK06266 transcription initiat 43.0 11 0.00025 33.9 1.0 17 9-25 116-132 (178)
126 PF01096 TFIIS_C: Transcriptio 42.5 12 0.00026 24.3 0.7 11 99-109 29-39 (39)
127 COG5236 Uncharacterized conser 41.9 18 0.00038 35.4 2.1 34 10-46 151-186 (493)
128 PF13451 zf-trcl: Probable zin 41.6 18 0.00039 24.8 1.5 24 8-31 2-25 (49)
129 PF09332 Mcm10: Mcm10 replicat 41.5 11 0.00024 37.5 0.7 39 9-47 251-293 (344)
130 KOG2186 Cell growth-regulating 41.2 14 0.00029 34.7 1.2 41 85-127 17-57 (276)
131 COG1996 RPC10 DNA-directed RNA 41.0 13 0.00029 25.4 0.8 28 430-469 6-33 (49)
132 PRK04023 DNA polymerase II lar 41.0 27 0.00057 39.6 3.5 53 375-474 625-677 (1121)
133 TIGR00244 transcriptional regu 40.4 18 0.00038 31.2 1.6 21 459-479 27-47 (147)
134 COG1592 Rubrerythrin [Energy p 40.3 16 0.00035 32.3 1.4 14 93-106 144-157 (166)
135 KOG0978 E3 ubiquitin ligase in 39.8 5.1 0.00011 43.5 -2.1 22 96-117 676-697 (698)
136 PF08790 zf-LYAR: LYAR-type C2 39.2 11 0.00024 22.4 0.2 19 377-396 1-19 (28)
137 COG1198 PriA Primosomal protei 38.6 21 0.00045 39.6 2.3 15 93-107 470-484 (730)
138 COG0068 HypF Hydrogenase matur 38.5 7.5 0.00016 42.1 -1.0 52 464-520 595-649 (750)
139 TIGR00373 conserved hypothetic 38.4 16 0.00035 32.2 1.2 19 8-26 107-125 (158)
140 PF12907 zf-met2: Zinc-binding 37.9 17 0.00037 23.8 0.9 29 99-127 2-34 (40)
141 PF13240 zinc_ribbon_2: zinc-r 37.5 22 0.00047 20.1 1.2 8 463-470 16-23 (23)
142 PF12013 DUF3505: Protein of u 37.1 12 0.00027 30.5 0.2 25 461-485 81-109 (109)
143 KOG2071 mRNA cleavage and poly 36.6 15 0.00033 38.9 0.8 29 457-485 415-443 (579)
144 COG2331 Uncharacterized protei 36.6 8.3 0.00018 28.8 -0.7 34 74-111 12-46 (82)
145 KOG0320 Predicted E3 ubiquitin 36.3 9.1 0.0002 33.9 -0.7 18 373-390 128-145 (187)
146 PRK12380 hydrogenase nickel in 35.7 20 0.00044 29.6 1.3 25 431-469 71-95 (113)
147 COG1571 Predicted DNA-binding 35.4 42 0.00091 34.4 3.7 60 433-508 353-412 (421)
148 KOG2785 C2H2-type Zn-finger pr 35.1 6.6 0.00014 39.1 -1.9 124 377-527 4-145 (390)
149 PF04216 FdhE: Protein involve 34.7 8 0.00017 37.9 -1.5 76 377-472 173-250 (290)
150 smart00531 TFIIE Transcription 34.6 15 0.00032 32.0 0.3 35 373-410 96-131 (147)
151 PF04959 ARS2: Arsenite-resist 34.0 22 0.00049 32.9 1.4 28 95-122 74-102 (214)
152 PF13878 zf-C2H2_3: zinc-finge 33.9 28 0.00062 22.8 1.5 24 99-122 14-39 (41)
153 KOG4377 Zn-finger protein [Gen 33.8 60 0.0013 32.8 4.3 106 9-123 270-428 (480)
154 PF15135 UPF0515: Uncharacteri 33.6 30 0.00066 32.4 2.2 74 22-113 91-170 (278)
155 smart00440 ZnF_C2C2 C2C2 Zinc 33.4 28 0.00061 22.7 1.4 11 99-109 29-39 (40)
156 TIGR00100 hypA hydrogenase nic 33.2 24 0.00052 29.2 1.4 25 432-470 72-96 (115)
157 smart00531 TFIIE Transcription 33.1 24 0.00051 30.7 1.4 12 98-109 123-134 (147)
158 PF06524 NOA36: NOA36 protein; 32.9 32 0.00069 32.4 2.2 91 373-484 139-233 (314)
159 PRK05580 primosome assembly pr 32.8 29 0.00063 38.5 2.3 12 96-107 419-430 (679)
160 COG1327 Predicted transcriptio 32.4 26 0.00057 30.2 1.5 18 459-476 27-44 (156)
161 COG3364 Zn-ribbon containing p 31.6 29 0.00063 27.6 1.5 17 10-26 2-18 (112)
162 COG3677 Transposase and inacti 31.6 32 0.0007 29.1 1.9 19 393-411 21-39 (129)
163 PF04438 zf-HIT: HIT zinc fing 31.0 16 0.00035 22.2 -0.0 12 460-471 13-24 (30)
164 TIGR00595 priA primosomal prot 30.7 30 0.00066 36.9 2.0 11 97-107 252-262 (505)
165 PTZ00255 60S ribosomal protein 30.3 25 0.00054 27.6 0.9 35 428-474 34-68 (90)
166 PRK00564 hypA hydrogenase nick 30.1 31 0.00066 28.7 1.5 26 431-470 72-98 (117)
167 PF01428 zf-AN1: AN1-like Zinc 29.7 21 0.00046 23.6 0.4 16 459-474 12-27 (43)
168 PF07975 C1_4: TFIIH C1-like d 29.6 15 0.00033 25.4 -0.3 30 9-45 20-49 (51)
169 PF07754 DUF1610: Domain of un 29.4 24 0.00051 20.3 0.5 10 459-468 15-24 (24)
170 COG0068 HypF Hydrogenase matur 28.8 28 0.0006 37.9 1.3 18 378-395 125-142 (750)
171 PRK03824 hypA hydrogenase nick 28.4 28 0.0006 29.8 1.0 12 458-469 105-116 (135)
172 PF15269 zf-C2H2_7: Zinc-finge 28.3 35 0.00076 22.6 1.2 21 99-119 21-41 (54)
173 PRK14873 primosome assembly pr 28.1 34 0.00074 37.8 1.9 43 377-467 384-429 (665)
174 PRK00432 30S ribosomal protein 27.9 37 0.00081 23.4 1.4 13 459-471 36-48 (50)
175 TIGR00280 L37a ribosomal prote 27.2 25 0.00054 27.6 0.5 35 428-474 33-67 (91)
176 KOG4124 Putative transcription 27.1 18 0.00039 35.5 -0.4 26 94-119 394-419 (442)
177 PRK03681 hypA hydrogenase nick 26.8 35 0.00075 28.2 1.3 26 431-469 71-96 (114)
178 KOG0317 Predicted E3 ubiquitin 26.8 24 0.00053 33.8 0.4 34 65-111 253-286 (293)
179 PRK12722 transcriptional activ 26.1 45 0.00098 30.1 1.9 24 433-468 137-162 (187)
180 KOG3408 U1-like Zn-finger-cont 26.1 18 0.00039 29.8 -0.6 26 373-398 54-79 (129)
181 KOG2071 mRNA cleavage and poly 25.6 41 0.00088 35.8 1.8 29 7-35 415-443 (579)
182 KOG0717 Molecular chaperone (D 25.2 20 0.00044 36.7 -0.4 23 460-482 460-482 (508)
183 PTZ00303 phosphatidylinositol 24.7 42 0.00092 36.7 1.7 14 377-390 461-474 (1374)
184 PF04423 Rad50_zn_hook: Rad50 24.4 27 0.0006 24.3 0.2 12 462-473 22-33 (54)
185 PF14446 Prok-RING_1: Prokaryo 24.4 46 0.001 23.4 1.3 29 431-473 6-34 (54)
186 PF10013 DUF2256: Uncharacteri 24.4 47 0.001 21.9 1.2 19 395-413 1-19 (42)
187 KOG2807 RNA polymerase II tran 24.1 1.1E+02 0.0024 30.0 4.2 25 98-122 345-369 (378)
188 KOG2636 Splicing factor 3a, su 24.1 48 0.001 33.9 1.9 29 91-119 394-423 (497)
189 PRK14559 putative protein seri 23.8 80 0.0017 34.7 3.6 12 462-473 43-54 (645)
190 PF14447 Prok-RING_4: Prokaryo 23.7 48 0.001 23.4 1.3 17 456-472 35-51 (55)
191 cd00924 Cyt_c_Oxidase_Vb Cytoc 23.6 37 0.00081 27.1 0.8 20 451-471 71-90 (97)
192 PRK03976 rpl37ae 50S ribosomal 23.5 31 0.00068 27.0 0.4 34 428-473 34-67 (90)
193 smart00661 RPOL9 RNA polymeras 23.5 56 0.0012 22.3 1.7 25 460-484 20-45 (52)
194 PHA02998 RNA polymerase subuni 23.4 45 0.00097 29.6 1.3 39 74-112 143-185 (195)
195 PTZ00303 phosphatidylinositol 23.4 54 0.0012 36.0 2.1 17 62-78 480-496 (1374)
196 PRK01343 zinc-binding protein; 23.3 51 0.0011 23.4 1.4 11 461-471 10-20 (57)
197 PF07282 OrfB_Zn_ribbon: Putat 23.3 52 0.0011 24.1 1.5 32 429-472 27-58 (69)
198 COG1773 Rubredoxin [Energy pro 23.2 34 0.00073 24.1 0.4 14 98-111 3-16 (55)
199 KOG0717 Molecular chaperone (D 22.9 41 0.00089 34.6 1.2 24 375-398 459-482 (508)
200 cd02335 ZZ_ADA2 Zinc finger, Z 22.8 46 0.001 22.7 1.1 27 458-484 13-45 (49)
201 PRK05580 primosome assembly pr 22.7 58 0.0013 36.2 2.4 22 431-469 409-430 (679)
202 PF12773 DZR: Double zinc ribb 22.3 1.3E+02 0.0029 20.2 3.4 8 461-468 30-37 (50)
203 KOG0978 E3 ubiquitin ligase in 22.3 19 0.00041 39.3 -1.4 33 433-480 666-698 (698)
204 KOG3362 Predicted BBOX Zn-fing 22.3 49 0.0011 28.2 1.3 36 428-482 116-151 (156)
205 PF03107 C1_2: C1 domain; Int 22.3 62 0.0013 19.4 1.5 8 460-467 15-22 (30)
206 PF13824 zf-Mss51: Zinc-finger 22.2 69 0.0015 22.6 1.8 15 457-471 11-25 (55)
207 PF01155 HypA: Hydrogenase exp 22.0 21 0.00046 29.4 -0.9 26 431-470 71-96 (113)
208 COG5152 Uncharacterized conser 22.0 26 0.00057 31.5 -0.4 14 9-22 195-208 (259)
209 PF11494 Ta0938: Ta0938; Inte 21.9 57 0.0012 25.7 1.5 40 7-52 11-50 (105)
210 PF01286 XPA_N: XPA protein N- 21.8 31 0.00067 21.7 0.0 15 462-476 5-19 (34)
211 KOG2482 Predicted C2H2-type Zn 21.6 29 0.00062 34.1 -0.2 26 459-484 194-221 (423)
212 KOG4317 Predicted Zn-finger pr 21.5 56 0.0012 31.7 1.7 35 429-481 6-40 (383)
213 PF09845 DUF2072: Zn-ribbon co 21.3 46 0.00099 28.1 0.9 12 460-471 1-12 (131)
214 COG3677 Transposase and inacti 21.1 54 0.0012 27.8 1.4 16 96-111 51-66 (129)
215 KOG2482 Predicted C2H2-type Zn 20.9 51 0.0011 32.4 1.3 29 10-38 195-225 (423)
216 PRK05978 hypothetical protein; 20.6 66 0.0014 28.0 1.8 11 101-111 55-65 (148)
217 KOG2593 Transcription initiati 20.6 35 0.00075 34.8 0.1 36 429-469 127-162 (436)
218 PRK12860 transcriptional activ 20.6 67 0.0015 29.1 1.9 23 433-467 137-161 (189)
219 PF04959 ARS2: Arsenite-resist 20.4 42 0.00091 31.1 0.6 30 7-36 74-103 (214)
220 COG3091 SprT Zn-dependent meta 20.2 48 0.001 28.7 0.9 35 71-107 114-149 (156)
No 1
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.97 E-value=1.9e-31 Score=273.04 Aligned_cols=61 Identities=18% Similarity=0.164 Sum_probs=57.2
Q ss_pred CcccccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhcccccccccCCCCCcc
Q 041528 430 KFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKRSHFVGGSEDKT 492 (527)
Q Consensus 430 ~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~H~~~~~~~~~ 492 (527)
++.|..|||.| .....|.+|+++|+|+|||.|.+|+++|.++.+|+.||++|+|.....+.
T Consensus 879 ~h~C~vCgk~F--sSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~srr 939 (958)
T KOG1074|consen 879 AHVCNVCGKQF--SSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSRR 939 (958)
T ss_pred hhhhccchhcc--cchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCccC
Confidence 45699999999 89999999999999999999999999999999999999999998887654
No 2
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=99.89 E-value=1.3e-23 Score=215.97 Aligned_cols=55 Identities=22% Similarity=0.284 Sum_probs=45.6
Q ss_pred cccCCCCCcc----cccchhhhhccCCCccccccccccccChhhHHHHHhhhcCCCCCC
Q 041528 74 GYVLRANPKR----TRRFVDSNTLTSQQEMVCKECGKVFQSLKALCGHMACHSEKDNKM 128 (527)
Q Consensus 74 ~~~c~~c~~~----~~~~~H~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~ 128 (527)
+.+|-+|.+. ..|.-|.|+|+|||||+|.|||++|.+++||+.||-+|.-+.+..
T Consensus 605 PNqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka~p~~R 663 (958)
T KOG1074|consen 605 PNQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKAKPPAR 663 (958)
T ss_pred ccceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhcccccccCcccc
Confidence 5566666654 355569999999999999999999999999999999998665544
No 3
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.86 E-value=3.2e-22 Score=202.00 Aligned_cols=82 Identities=18% Similarity=0.315 Sum_probs=74.9
Q ss_pred cCCccccccccccccCccccccccccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccccccc
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKR 452 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~ 452 (527)
.++.|.|+.|.|+|...+.|.+|+=-|+|.++ |.|.+|.|.| ..+..|.-|+
T Consensus 891 e~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRP--------------------------yqC~iCkKAF--KHKHHLtEHk 942 (1007)
T KOG3623|consen 891 EDGMYACDQCDKAFQKQSSLARHKYEHSGQRP--------------------------YQCIICKKAF--KHKHHLTEHK 942 (1007)
T ss_pred ccccchHHHHHHHHHhhHHHHHhhhhhcCCCC--------------------------cccchhhHhh--hhhhhhhhhh
Confidence 46899999999999999999999999998553 4588999999 8999999999
Q ss_pred cccCCCCCccCCCcCccccchhhhcccccc
Q 041528 453 LGSKKSKGHECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 453 ~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
|.|.|||||.|+.|+|+|..+++.-.||.-
T Consensus 943 RLHSGEKPfQCdKClKRFSHSGSYSQHMNH 972 (1007)
T KOG3623|consen 943 RLHSGEKPFQCDKCLKRFSHSGSYSQHMNH 972 (1007)
T ss_pred hhccCCCcchhhhhhhhcccccchHhhhcc
Confidence 999999999999999999999999999973
No 4
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.83 E-value=1.9e-21 Score=177.76 Aligned_cols=135 Identities=21% Similarity=0.230 Sum_probs=122.2
Q ss_pred ccccccCcccccccCCCChhhhcC-----CcccCCccccccccccccCccccccccccCCCCCCCCcccccccCCCcCcC
Q 041528 346 RASTKHGSRKRAKNDSSSPQIFRN-----NAQKRSQFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETD 420 (527)
Q Consensus 346 ~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~ 420 (527)
.....+.|..|++..++.+.|..| .....+.+.|++|||.|.+--+|..|+|+|+-.-.|.+|++.|+..=+|.+
T Consensus 126 ~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQG 205 (279)
T KOG2462|consen 126 AKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQG 205 (279)
T ss_pred ccCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhc
Confidence 345577888999998888888776 234578999999999999999999999999987899999999999999999
Q ss_pred CCCCCCCCCCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhcccccc
Q 041528 421 SFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 421 ~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
|.+.+.+.++|.|++|+|.| +.+++|+-|+.+|.+.|+|+|+.|+|.|..++.|.+|...
T Consensus 206 HiRTHTGEKPF~C~hC~kAF--ADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES 265 (279)
T KOG2462|consen 206 HIRTHTGEKPFSCPHCGKAF--ADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSES 265 (279)
T ss_pred ccccccCCCCccCCcccchh--cchHHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhh
Confidence 99999999999999999999 8999999999999999999999999999999999999753
No 5
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=99.82 E-value=2.8e-21 Score=176.63 Aligned_cols=111 Identities=17% Similarity=0.203 Sum_probs=102.6
Q ss_pred cCCccccccccccccCccccccccccCCC-----CCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCcc
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWGHTASHSK-----INGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLST 447 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~H~~~H~~-----~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~ 447 (527)
....|.|..|||.+.+.++|.+|+.+|-. -..|+.|++.+.....|+.|..++. -+..|.+|||.| +..++
T Consensus 127 ~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaF--SRPWL 202 (279)
T KOG2462|consen 127 KHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHT--LPCECGICGKAF--SRPWL 202 (279)
T ss_pred cCCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccC--CCcccccccccc--cchHH
Confidence 45779999999999999999999999983 2399999999999999999988876 466799999999 99999
Q ss_pred ccccccccCCCCCccCCCcCccccchhhhcccccccccCC
Q 041528 448 NVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKRSHFVGG 487 (527)
Q Consensus 448 l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~H~~~~ 487 (527)
|+-|.|+|||||||.|+.|+|+|..+++|.-||+||.+..
T Consensus 203 LQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K 242 (279)
T KOG2462|consen 203 LQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVK 242 (279)
T ss_pred hhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCc
Confidence 9999999999999999999999999999999999999865
No 6
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.59 E-value=4.6e-17 Score=152.38 Aligned_cols=80 Identities=25% Similarity=0.390 Sum_probs=63.9
Q ss_pred CCccccccccccccCccccccccccCCCCC-CCCc--ccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccccc
Q 041528 374 RSQFKCLTCNKVFHSPRSLWGHTASHSKIN-GCCE--SINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVD 450 (527)
Q Consensus 374 ~~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~-~C~~--c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~ 450 (527)
.+||+|+.|.+.|...+.|..|..+|.+.. .|.. |.++| .++..++.
T Consensus 290 dkpfKCd~Cd~~c~~esdL~kH~~~HS~~~y~C~h~~C~~s~------------------------------r~~~q~~~ 339 (467)
T KOG3608|consen 290 DKPFKCDECDTRCVRESDLAKHVQVHSKTVYQCEHPDCHYSV------------------------------RTYTQMRR 339 (467)
T ss_pred CCCccccchhhhhccHHHHHHHHHhccccceecCCCCCcHHH------------------------------HHHHHHHH
Confidence 689999999999999999999999999754 7663 55555 45555556
Q ss_pred cccc-cC--CCCCccCCCcCccccchhhhccc-cccc
Q 041528 451 KRLG-SK--KSKGHECPFCFRVFKSGQALGGH-KRSH 483 (527)
Q Consensus 451 h~~~-Ht--~ekp~~C~iC~k~F~~~~~L~~H-~r~H 483 (527)
|++- |. .+-+|+|..|++.|++..+|..| ||.|
T Consensus 340 H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH 376 (467)
T KOG3608|consen 340 HFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKH 376 (467)
T ss_pred HHHHhccCCCCCceeeecchhhhccchhHHHHHHHhh
Confidence 6554 42 46789999999999999999999 4456
No 7
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.54 E-value=3.2e-16 Score=135.94 Aligned_cols=85 Identities=22% Similarity=0.354 Sum_probs=76.6
Q ss_pred cCCccccccccccccCccccccccccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccccccc
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKR 452 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~ 452 (527)
....|.|.+|||.|.....|.+|++.|...+ ++.|..|||.| ...-+|++|+
T Consensus 114 d~d~ftCrvCgK~F~lQRmlnrh~kch~~vk--------------------------r~lct~cgkgf--ndtfdlkrh~ 165 (267)
T KOG3576|consen 114 DQDSFTCRVCGKKFGLQRMLNRHLKCHSDVK--------------------------RHLCTFCGKGF--NDTFDLKRHT 165 (267)
T ss_pred CCCeeeeehhhhhhhHHHHHHHHhhhccHHH--------------------------HHHHhhccCcc--cchhhhhhhh
Confidence 4578999999999999999999999998744 56688999999 8999999999
Q ss_pred cccCCCCCccCCCcCccccchhhhccccc-cccc
Q 041528 453 LGSKKSKGHECPFCFRVFKSGQALGGHKR-SHFV 485 (527)
Q Consensus 453 ~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r-~H~~ 485 (527)
|+|||.+||+|..|+|+|+++-+|..|++ +|--
T Consensus 166 rthtgvrpykc~~c~kaftqrcsleshl~kvhgv 199 (267)
T KOG3576|consen 166 RTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGV 199 (267)
T ss_pred ccccCccccchhhhhHHHHhhccHHHHHHHHcCc
Confidence 99999999999999999999999999965 5643
No 8
>KOG3608 consensus Zn finger proteins [General function prediction only]
Probab=99.49 E-value=1.3e-15 Score=142.77 Aligned_cols=110 Identities=16% Similarity=0.161 Sum_probs=99.9
Q ss_pred ccccccccccccCccccccccccCCCCCCCCcccccccCCCcCcCCCCCC-CCCCCcccccCCCCcccccCccccccccc
Q 041528 376 QFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETDSFPVP-MPNSKFCKSVNGKTPIAQNLSTNVDKRLG 454 (527)
Q Consensus 376 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~-~~~~~~~c~~C~K~f~~~~~~~l~~h~~~ 454 (527)
+|.|..|-|.|.+...|..|++-|..-++|+.|..+....+.|..|.+.. ....+++|..|.++| .+.+.|.+|..+
T Consensus 237 ~fqC~~C~KrFaTeklL~~Hv~rHvn~ykCplCdmtc~~~ssL~~H~r~rHs~dkpfKCd~Cd~~c--~~esdL~kH~~~ 314 (467)
T KOG3608|consen 237 SFQCAQCFKRFATEKLLKSHVVRHVNCYKCPLCDMTCSSASSLTTHIRYRHSKDKPFKCDECDTRC--VRESDLAKHVQV 314 (467)
T ss_pred chHHHHHHHHHhHHHHHHHHHHHhhhcccccccccCCCChHHHHHHHHhhhccCCCccccchhhhh--ccHHHHHHHHHh
Confidence 58999999999999999999999999999999999999999898887764 367899999999999 899999999999
Q ss_pred cCCCCCccCCC--cCccccchhhhcccccccccCCC
Q 041528 455 SKKSKGHECPF--CFRVFKSGQALGGHKRSHFVGGS 488 (527)
Q Consensus 455 Ht~ekp~~C~i--C~k~F~~~~~L~~H~r~H~~~~~ 488 (527)
|. +..|.|+. |...|++...|.+|++.|..+.+
T Consensus 315 HS-~~~y~C~h~~C~~s~r~~~q~~~H~~evhEg~n 349 (467)
T KOG3608|consen 315 HS-KTVYQCEHPDCHYSVRTYTQMRRHFLEVHEGNN 349 (467)
T ss_pred cc-ccceecCCCCCcHHHHHHHHHHHHHHHhccCCC
Confidence 99 88999999 99999999999999998765444
No 9
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=99.34 E-value=1.5e-13 Score=139.98 Aligned_cols=80 Identities=16% Similarity=0.301 Sum_probs=71.1
Q ss_pred CCceecccCCCccCCchhHHHHhhhhcCCCCccccccccccccccccccccCCcccccccccCCCccccCCCCCcccccc
Q 041528 8 KKLFVCKYCNKRYPCGKSLGGHIRTHMNNGNSAEAEGEGEVKLNIDKIFSGRNIKKDSCFEAGGQSGYVLRANPKRTRRF 87 (527)
Q Consensus 8 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~p~~~C~~C~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~c~~c~~~~~~~ 87 (527)
+-.|.|++|+|+|...++|-||...|+|.||| +| .+|.|.|.. ++.|.
T Consensus 892 ~gmyaCDqCDK~FqKqSSLaRHKYEHsGqRPy-qC------------------------~iCkKAFKH-------KHHLt 939 (1007)
T KOG3623|consen 892 DGMYACDQCDKAFQKQSSLARHKYEHSGQRPY-QC------------------------IICKKAFKH-------KHHLT 939 (1007)
T ss_pred cccchHHHHHHHHHhhHHHHHhhhhhcCCCCc-cc------------------------chhhHhhhh-------hhhhh
Confidence 45899999999999999999999999999999 44 455566655 45677
Q ss_pred hhhhhccCCCccccccccccccChhhHHHHHh
Q 041528 88 VDSNTLTSQQEMVCKECGKVFQSLKALCGHMA 119 (527)
Q Consensus 88 ~H~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~~ 119 (527)
.|+|.|.|+|||+|+-|+|+|.+.+...+||.
T Consensus 940 EHkRLHSGEKPfQCdKClKRFSHSGSYSQHMN 971 (1007)
T KOG3623|consen 940 EHKRLHSGEKPFQCDKCLKRFSHSGSYSQHMN 971 (1007)
T ss_pred hhhhhccCCCcchhhhhhhhcccccchHhhhc
Confidence 89999999999999999999999999999996
No 10
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=99.34 E-value=1.7e-13 Score=119.12 Aligned_cols=83 Identities=22% Similarity=0.389 Sum_probs=73.7
Q ss_pred CCceecccCCCccCCchhHHHHhhhhcCCCCccccccccccccccccccccCCcccccccccCCCccccCCCCCcccccc
Q 041528 8 KKLFVCKYCNKRYPCGKSLGGHIRTHMNNGNSAEAEGEGEVKLNIDKIFSGRNIKKDSCFEAGGQSGYVLRANPKRTRRF 87 (527)
Q Consensus 8 ~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~p~~~C~~C~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~c~~c~~~~~~~ 87 (527)
...|.|.+|+|.|.--.-|.+|++.|...+-| -|..||+.|.- .|.|+
T Consensus 115 ~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~-------------------------lct~cgkgfnd-------tfdlk 162 (267)
T KOG3576|consen 115 QDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRH-------------------------LCTFCGKGFND-------TFDLK 162 (267)
T ss_pred CCeeeeehhhhhhhHHHHHHHHhhhccHHHHH-------------------------HHhhccCcccc-------hhhhh
Confidence 45799999999999999999999999776554 77888888876 57999
Q ss_pred hhhhhccCCCccccccccccccChhhHHHHH-hhhc
Q 041528 88 VDSNTLTSQQEMVCKECGKVFQSLKALCGHM-ACHS 122 (527)
Q Consensus 88 ~H~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~-~~H~ 122 (527)
+|.|+|+|.+||+|.+|+++|.+.-.|..|. ++|.
T Consensus 163 rh~rthtgvrpykc~~c~kaftqrcsleshl~kvhg 198 (267)
T KOG3576|consen 163 RHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHG 198 (267)
T ss_pred hhhccccCccccchhhhhHHHHhhccHHHHHHHHcC
Confidence 9999999999999999999999999999999 4554
No 11
>PHA00733 hypothetical protein
Probab=98.82 E-value=7.9e-10 Score=93.53 Aligned_cols=85 Identities=9% Similarity=0.067 Sum_probs=68.4
Q ss_pred cCCccccccccccccCccccccc--cccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccccc
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWGH--TASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVD 450 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~H--~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~ 450 (527)
..+++.|.+|++.|.....|..| ++.|.. .....+|.|+.||+.| .....|..
T Consensus 37 ~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~-----------------------~~~~kPy~C~~Cgk~F--ss~s~L~~ 91 (128)
T PHA00733 37 EQKRLIRAVVKTLIYNPQLLDESSYLYKLLT-----------------------SKAVSPYVCPLCLMPF--SSSVSLKQ 91 (128)
T ss_pred hhhhHHHHHHhhhccChhhhcchHHHHhhcc-----------------------cCCCCCccCCCCCCcC--CCHHHHHH
Confidence 46889999999999999988887 333321 1123456788999999 88899999
Q ss_pred cccccCCCCCccCCCcCccccchhhhcccccccc
Q 041528 451 KRLGSKKSKGHECPFCFRVFKSGQALGGHKRSHF 484 (527)
Q Consensus 451 h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~H~ 484 (527)
|+++| +.+|.|++|+++|....+|..|++...
T Consensus 92 H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h 123 (128)
T PHA00733 92 HIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKH 123 (128)
T ss_pred HHhcC--CcCccCCCCCCccCCHHHHHHHHHHhc
Confidence 99987 468999999999999999999987643
No 12
>PHA02768 hypothetical protein; Provisional
Probab=98.72 E-value=2e-09 Score=74.56 Aligned_cols=44 Identities=7% Similarity=-0.004 Sum_probs=40.1
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhcc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGG 478 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~ 478 (527)
|.|+.|||.| +....|..|+++|+ +||+|..|+|.|.+++.|..
T Consensus 6 y~C~~CGK~F--s~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s~l~~ 49 (55)
T PHA02768 6 YECPICGEIY--IKRKSMITHLRKHN--TNLKLSNCKRISLRTGEYIE 49 (55)
T ss_pred cCcchhCCee--ccHHHHHHHHHhcC--CcccCCcccceecccceeEE
Confidence 5699999999 89999999999999 79999999999998888763
No 13
>PHA02768 hypothetical protein; Provisional
Probab=98.72 E-value=3e-09 Score=73.76 Aligned_cols=43 Identities=14% Similarity=0.277 Sum_probs=35.5
Q ss_pred ccccccccccccCccccccccccCCCCCCCCcccccccCCCcC
Q 041528 376 QFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRE 418 (527)
Q Consensus 376 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~ 418 (527)
-|+|+.|||.|...++|..||++|+...+|..|++.|...+.|
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~~s~l 47 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLRTGEY 47 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceeccccee
Confidence 4899999999999999999999999767777666666544433
No 14
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.62 E-value=3.6e-09 Score=62.66 Aligned_cols=26 Identities=19% Similarity=0.393 Sum_probs=23.6
Q ss_pred cccccccccCCCCCccCCCcCccccc
Q 041528 447 TNVDKRLGSKKSKGHECPFCFRVFKS 472 (527)
Q Consensus 447 ~l~~h~~~Ht~ekp~~C~iC~k~F~~ 472 (527)
+|..|+++|+|+|||.|++|+++|.+
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 36789999999999999999999974
No 15
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.58 E-value=1.3e-08 Score=105.46 Aligned_cols=101 Identities=15% Similarity=0.174 Sum_probs=84.0
Q ss_pred cCCccccccccccccCccccccccccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccc---------
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQ--------- 443 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~--------- 443 (527)
.+..+.|+.||+.|. ...|..|+++|+....|+ |++.+ .+..|..|...+++...+.|++|++.| .
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v--~~g~~~~d~~ 524 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKVFHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV--QAGGSAMDVR 524 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHhcCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc--ccCccccchh
Confidence 346689999999996 688999999988888999 99654 668888888888889999999999999 4
Q ss_pred -cCccccccccccCCCCCccCCCcCccccchhhhcccc
Q 041528 444 -NLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHK 480 (527)
Q Consensus 444 -~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~ 480 (527)
....|..|+.++ |.+++.|..||+.|..+ -|..|+
T Consensus 525 d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~ 560 (567)
T PLN03086 525 DRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQ 560 (567)
T ss_pred hhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHH
Confidence 235788898886 89999999999998763 456664
No 16
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.50 E-value=3.3e-08 Score=95.88 Aligned_cols=113 Identities=20% Similarity=0.252 Sum_probs=74.8
Q ss_pred CccccccccccccCccccccccccCCCCC-------------------CCCcccccccCCCcCcCCC-CCCCCCCCcccc
Q 041528 375 SQFKCLTCNKVFHSPRSLWGHTASHSKIN-------------------GCCESINESSENSRETDSF-PVPMPNSKFCKS 434 (527)
Q Consensus 375 ~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~-------------------~C~~c~~~f~~~~~~~~~~-~~~~~~~~~~c~ 434 (527)
..|.|.+|||.|.....|+.|+.+|..-- .|..|.-.+.....+.... -.-.......|.
T Consensus 355 gi~~C~~C~KkFrRqAYLrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp 434 (500)
T KOG3993|consen 355 GIFSCHTCGKKFRRQAYLRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPP 434 (500)
T ss_pred ceeecHHhhhhhHHHHHHHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCC
Confidence 57999999999999999999999988421 1111111111111111110 011122344688
Q ss_pred cCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhccccc-ccccCCCC
Q 041528 435 VNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKR-SHFVGGSE 489 (527)
Q Consensus 435 ~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r-~H~~~~~~ 489 (527)
+||-.| +.++.-.-+.+.-..+--|.|.+|--+|.+...|.+|.. .|..+..+
T Consensus 435 ~~~~pp--sss~~sgg~~rlg~~~q~f~~ky~~atfyss~~ltrhin~~Hpse~rq 488 (500)
T KOG3993|consen 435 YDGSPP--SSSGSSGGYGRLGIAEQGFTCKYCPATFYSSPGLTRHINKCHPSELRQ 488 (500)
T ss_pred CCCCCc--ccCCCCCccccccchhhccccccchHhhhcCcchHhHhhhcChHHhhh
Confidence 999888 666666666655555778999999999999999999965 58776653
No 17
>PHA00733 hypothetical protein
Probab=98.44 E-value=8e-08 Score=81.34 Aligned_cols=82 Identities=12% Similarity=0.087 Sum_probs=59.6
Q ss_pred CCceecccCCCccCCchhHHHH--hhh---hcCCCCccccccccccccccccccccCCcccccccccCCCccccCCCCCc
Q 041528 8 KKLFVCKYCNKRYPCGKSLGGH--IRT---HMNNGNSAEAEGEGEVKLNIDKIFSGRNIKKDSCFEAGGQSGYVLRANPK 82 (527)
Q Consensus 8 ~~~~~C~~C~k~f~~~~~L~~H--~~~---H~~~~p~~~C~~C~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~c~~c~~ 82 (527)
.+++.|.+|.+.|.....|..| ++. +.+.+|| .|..|++.|....
T Consensus 38 ~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy-------------------------~C~~Cgk~Fss~s----- 87 (128)
T PHA00733 38 QKRLIRAVVKTLIYNPQLLDESSYLYKLLTSKAVSPY-------------------------VCPLCLMPFSSSV----- 87 (128)
T ss_pred hhhHHHHHHhhhccChhhhcchHHHHhhcccCCCCCc-------------------------cCCCCCCcCCCHH-----
Confidence 4678899999888887777766 222 2234454 6666666665532
Q ss_pred ccccchhhhhccCCCccccccccccccChhhHHHHHhhhcC
Q 041528 83 RTRRFVDSNTLTSQQEMVCKECGKVFQSLKALCGHMACHSE 123 (527)
Q Consensus 83 ~~~~~~H~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~ 123 (527)
.|..|++.| ..+|.|++|++.|.....|..|++..++
T Consensus 88 --~L~~H~r~h--~~~~~C~~CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 88 --SLKQHIRYT--EHSKVCPVCGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred --HHHHHHhcC--CcCccCCCCCCccCCHHHHHHHHHHhcC
Confidence 566788776 4579999999999999999999966553
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=98.40 E-value=8.1e-08 Score=56.86 Aligned_cols=25 Identities=28% Similarity=0.438 Sum_probs=23.0
Q ss_pred cchhhhhccCCCccccccccccccC
Q 041528 86 RFVDSNTLTSQQEMVCKECGKVFQS 110 (527)
Q Consensus 86 ~~~H~~~h~~~k~~~C~~Cgk~F~~ 110 (527)
|..|+++|+|++||+|++|+++|.+
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEESS
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeCc
Confidence 5679999999999999999999974
No 19
>PLN03086 PRLI-interacting factor K; Provisional
Probab=98.39 E-value=2.9e-07 Score=95.62 Aligned_cols=109 Identities=13% Similarity=0.157 Sum_probs=68.9
Q ss_pred CCCceecccCCCccCCchhHHHHhhhhcCCCCcccccccccccccc-cccccc--CCcccccccccCCCccccCC---CC
Q 041528 7 KKKLFVCKYCNKRYPCGKSLGGHIRTHMNNGNSAEAEGEGEVKLNI-DKIFSG--RNIKKDSCFEAGGQSGYVLR---AN 80 (527)
Q Consensus 7 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~p~~~C~~C~~~~~~~-~~~~~~--~~~~~~~c~~c~~~~~~~c~---~c 80 (527)
-++.+.|++|++.|. ...|..|+++|+ +|+ .|+ ||+.+... ...|.. -..+++.|..|+..+...-. .-
T Consensus 450 l~~H~~C~~Cgk~f~-~s~LekH~~~~H--kpv-~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~~~d~~ 524 (567)
T PLN03086 450 AKNHVHCEKCGQAFQ-QGEMEKHMKVFH--EPL-QCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQAGGSAMDVR 524 (567)
T ss_pred cccCccCCCCCCccc-hHHHHHHHHhcC--CCc-cCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccccCccccchh
Confidence 356789999999996 678999999985 788 999 97533222 112211 11234444444444321000 00
Q ss_pred CcccccchhhhhccCCCccccccccccccChhhHHHHH-hhhc
Q 041528 81 PKRTRRFVDSNTLTSQQEMVCKECGKVFQSLKALCGHM-ACHS 122 (527)
Q Consensus 81 ~~~~~~~~H~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~-~~H~ 122 (527)
.....|..|+..+ |.+++.|..||+.|..+ .|..|+ .+|.
T Consensus 525 d~~s~Lt~HE~~C-G~rt~~C~~Cgk~Vrlr-dm~~H~~~~h~ 565 (567)
T PLN03086 525 DRLRGMSEHESIC-GSRTAPCDSCGRSVMLK-EMDIHQIAVHQ 565 (567)
T ss_pred hhhhhHHHHHHhc-CCcceEccccCCeeeeh-hHHHHHHHhhc
Confidence 0011355688886 89999999999998876 778887 5564
No 20
>PHA00732 hypothetical protein
Probab=98.35 E-value=1.6e-07 Score=71.81 Aligned_cols=25 Identities=28% Similarity=0.429 Sum_probs=19.2
Q ss_pred ccccccccccccCcccccccccc-CC
Q 041528 376 QFKCLTCNKVFHSPRSLWGHTAS-HS 400 (527)
Q Consensus 376 ~~~C~~Cgk~F~~~~~L~~H~~~-H~ 400 (527)
||.|.+||+.|.+.++|..|++. |+
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~ 26 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT 26 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC
Confidence 47788888888888888888774 44
No 21
>PHA00616 hypothetical protein
Probab=98.28 E-value=2.3e-07 Score=61.17 Aligned_cols=34 Identities=15% Similarity=0.259 Sum_probs=31.6
Q ss_pred ceecccCCCccCCchhHHHHhhhhcCCCCcccccc
Q 041528 10 LFVCKYCNKRYPCGKSLGGHIRTHMNNGNSAEAEG 44 (527)
Q Consensus 10 ~~~C~~C~k~f~~~~~L~~H~~~H~~~~p~~~C~~ 44 (527)
||+|..||++|...++|.+|++.|++++++ .|+.
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~-~~~~ 34 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKL-TLEY 34 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCcc-ceeE
Confidence 699999999999999999999999999998 6654
No 22
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=98.12 E-value=3e-07 Score=89.38 Aligned_cols=110 Identities=15% Similarity=0.166 Sum_probs=56.3
Q ss_pred CccccccccccccCcccccccc--ccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcc--cccCCCCcccccCccccc
Q 041528 375 SQFKCLTCNKVFHSPRSLWGHT--ASHSKINGCCESINESSENSRETDSFPVPMPNSKFC--KSVNGKTPIAQNLSTNVD 450 (527)
Q Consensus 375 ~~~~C~~Cgk~F~~~~~L~~H~--~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~--c~~C~K~f~~~~~~~l~~ 450 (527)
+-|.|..|.-.|...-.|.+|. ||-.-||+|++|.+.|+--..|..|.+-+-+..... =..=.|.-. ......+-
T Consensus 266 GdyiCqLCK~kYeD~F~LAQHrC~RIV~vEYrCPEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~-~~rae~~e 344 (500)
T KOG3993|consen 266 GDYICQLCKEKYEDAFALAQHRCPRIVHVEYRCPECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAV-ETRAEVQE 344 (500)
T ss_pred HHHHHHHHHHhhhhHHHHhhccCCeeEEeeecCCcccccccCchhhhhhhcccCCchhhhhcCCCChhhhh-hhhhhhhh
Confidence 4577777777777777777774 555556666666666653333333322211111000 000000000 00000000
Q ss_pred cccc--cCCCCCccCCCcCccccchhhhccccccccc
Q 041528 451 KRLG--SKKSKGHECPFCFRVFKSGQALGGHKRSHFV 485 (527)
Q Consensus 451 h~~~--Ht~ekp~~C~iC~k~F~~~~~L~~H~r~H~~ 485 (527)
-.+. -..+--|.|.+|+|.|.+...|+.|+-+|.-
T Consensus 345 a~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 345 AERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred ccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 0000 0112369999999999999999999888753
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=97.99 E-value=9.3e-07 Score=50.83 Aligned_cols=23 Identities=39% Similarity=0.756 Sum_probs=21.8
Q ss_pred ccCCCcCccccchhhhccccccc
Q 041528 461 HECPFCFRVFKSGQALGGHKRSH 483 (527)
Q Consensus 461 ~~C~iC~k~F~~~~~L~~H~r~H 483 (527)
|+|++|++.|.+...|..||++|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 78999999999999999999986
No 24
>PHA00616 hypothetical protein
Probab=97.93 E-value=4.8e-06 Score=54.97 Aligned_cols=31 Identities=19% Similarity=0.477 Sum_probs=28.6
Q ss_pred ccccccccccccChhhHHHHHhhhcCCCCCC
Q 041528 98 EMVCKECGKVFQSLKALCGHMACHSEKDNKM 128 (527)
Q Consensus 98 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~~ 128 (527)
||+|..||+.|...++|..|++.|+++++..
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~ 31 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccc
Confidence 6999999999999999999999999987653
No 25
>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=97.82 E-value=9.9e-06 Score=46.47 Aligned_cols=23 Identities=43% Similarity=0.687 Sum_probs=21.8
Q ss_pred cccccccccccChhhHHHHHhhh
Q 041528 99 MVCKECGKVFQSLKALCGHMACH 121 (527)
Q Consensus 99 ~~C~~Cgk~F~~~~~L~~H~~~H 121 (527)
|+|++|+++|.+...|..|++.|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 78999999999999999999876
No 26
>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=97.81 E-value=4e-06 Score=59.54 Aligned_cols=51 Identities=22% Similarity=0.203 Sum_probs=42.0
Q ss_pred CcccccCCCCcccccCccccccccccCCC-CCccCCCcCccccchhhhcccccccc
Q 041528 430 KFCKSVNGKTPIAQNLSTNVDKRLGSKKS-KGHECPFCFRVFKSGQALGGHKRSHF 484 (527)
Q Consensus 430 ~~~c~~C~K~f~~~~~~~l~~h~~~Ht~e-kp~~C~iC~k~F~~~~~L~~H~r~H~ 484 (527)
.|.|++||+.| ....++.|....|..+ +.+.||||...++. +|..||+++.
T Consensus 2 ~f~CP~C~~~~--~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~~--~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKGF--SESSLVEHCEDEHRSESKNVVCPICSSRVTD--NLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCcc--CHHHHHHHHHhHCcCCCCCccCCCchhhhhh--HHHHHHHHhc
Confidence 47799999987 7777777778888876 68999999997664 9999988754
No 27
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.80 E-value=1e-05 Score=75.92 Aligned_cols=66 Identities=27% Similarity=0.440 Sum_probs=50.1
Q ss_pred CCcccccc--ccccccCcccccccccc-CCCCC----CCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCc
Q 041528 374 RSQFKCLT--CNKVFHSPRSLWGHTAS-HSKIN----GCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLS 446 (527)
Q Consensus 374 ~~~~~C~~--Cgk~F~~~~~L~~H~~~-H~~~~----~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~ 446 (527)
.|||+|.+ |.|.|+....|+.||.- |-..+ +-++-...|
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F---------------------------------- 392 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIF---------------------------------- 392 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccc----------------------------------
Confidence 49999998 99999999999999864 54333 222222222
Q ss_pred cccccccccCCCCCccCCCcCccccchhhhccccc
Q 041528 447 TNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKR 481 (527)
Q Consensus 447 ~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r 481 (527)
-...|||+|++|+|++...--|+.|.+
T Consensus 393 --------~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 393 --------SAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred --------cccCCceeccccchhhccCccceeccc
Confidence 134799999999999999999999964
No 28
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.53 E-value=2.2e-05 Score=47.02 Aligned_cols=26 Identities=46% Similarity=0.613 Sum_probs=24.2
Q ss_pred CccCCCcCccccchhhhccccccccc
Q 041528 460 GHECPFCFRVFKSGQALGGHKRSHFV 485 (527)
Q Consensus 460 p~~C~iC~k~F~~~~~L~~H~r~H~~ 485 (527)
||+|.+|++.|.+...|..|++.|..
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 68999999999999999999999864
No 29
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.47 E-value=2.5e-05 Score=46.76 Aligned_cols=26 Identities=38% Similarity=0.687 Sum_probs=24.1
Q ss_pred ccccccccccccCccccccccccCCC
Q 041528 376 QFKCLTCNKVFHSPRSLWGHTASHSK 401 (527)
Q Consensus 376 ~~~C~~Cgk~F~~~~~L~~H~~~H~~ 401 (527)
+|.|.+|++.|.+..+|..|++.|.+
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhcC
Confidence 58999999999999999999999864
No 30
>PHA00732 hypothetical protein
Probab=97.46 E-value=7.4e-05 Score=57.24 Aligned_cols=39 Identities=18% Similarity=0.221 Sum_probs=32.4
Q ss_pred ceecccCCCccCCchhHHHHhhh-hcCCCCcccccccccccccc
Q 041528 10 LFVCKYCNKRYPCGKSLGGHIRT-HMNNGNSAEAEGEGEVKLNI 52 (527)
Q Consensus 10 ~~~C~~C~k~f~~~~~L~~H~~~-H~~~~p~~~C~~C~~~~~~~ 52 (527)
||.|..|++.|.....|.+|++. |. ++ .|+.|++.|...
T Consensus 1 py~C~~Cgk~F~s~s~Lk~H~r~~H~---~~-~C~~CgKsF~~l 40 (79)
T PHA00732 1 MFKCPICGFTTVTLFALKQHARRNHT---LT-KCPVCNKSYRRL 40 (79)
T ss_pred CccCCCCCCccCCHHHHHHHhhcccC---CC-ccCCCCCEeCCh
Confidence 68999999999999999999985 65 46 888887766544
No 31
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.45 E-value=3.1e-05 Score=62.89 Aligned_cols=73 Identities=26% Similarity=0.429 Sum_probs=22.1
Q ss_pred ccccccccccCccccccccccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccccccccccCC
Q 041528 378 KCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKRLGSKK 457 (527)
Q Consensus 378 ~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ 457 (527)
+|.+|+..|.+...|..||...++...-. .+.+ .....+..+.+. .-
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~------------------------------~~~l--~~~~~~~~~~~~-~~ 47 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPD------------------------------QKYL--VDPNRLLNYLRK-KV 47 (100)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Ccccccccccccccccccccccccccccc------------------------------cccc--cccccccccccc-cc
Confidence 59999999999999999997766532100 0000 011111111111 11
Q ss_pred CCCccCCCcCccccchhhhccccccc
Q 041528 458 SKGHECPFCFRVFKSGQALGGHKRSH 483 (527)
Q Consensus 458 ekp~~C~iC~k~F~~~~~L~~H~r~H 483 (527)
...+.|.+|++.|.+...|..||+.+
T Consensus 48 ~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 48 KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 23799999999999999999999975
No 32
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.36 E-value=9.5e-05 Score=69.58 Aligned_cols=70 Identities=23% Similarity=0.350 Sum_probs=48.3
Q ss_pred CCceeccc--CCCccCCchhHHHHhhh-hcCCCCccccccccccccccccccccCCcccccccccCCCccccCCCCCccc
Q 041528 8 KKLFVCKY--CNKRYPCGKSLGGHIRT-HMNNGNSAEAEGEGEVKLNIDKIFSGRNIKKDSCFEAGGQSGYVLRANPKRT 84 (527)
Q Consensus 8 ~~~~~C~~--C~k~f~~~~~L~~H~~~-H~~~~p~~~C~~C~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~c~~c~~~~ 84 (527)
+|||+|++ |+|.|++...|+.|+.- |-..+.. ... .-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~-----------------~~p--------~p--------------- 386 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLH-----------------ENP--------SP--------------- 386 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccC-----------------CCC--------Cc---------------
Confidence 59999986 99999999999999743 3222111 000 00
Q ss_pred ccchhhhhccCCCccccccccccccChhhHHHHHh
Q 041528 85 RRFVDSNTLTSQQEMVCKECGKVFQSLKALCGHMA 119 (527)
Q Consensus 85 ~~~~H~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~~ 119 (527)
..|.-.-...|||.|++|+|+|+....|+-|..
T Consensus 387 --~~~~~F~~~~KPYrCevC~KRYKNlNGLKYHr~ 419 (423)
T COG5189 387 --EKMNIFSAKDKPYRCEVCDKRYKNLNGLKYHRK 419 (423)
T ss_pred --cccccccccCCceeccccchhhccCccceeccc
Confidence 011111245789999999999999999999874
No 33
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=97.35 E-value=0.00012 Score=42.14 Aligned_cols=24 Identities=42% Similarity=0.738 Sum_probs=20.2
Q ss_pred cccccccccccChhhHHHHHhhhc
Q 041528 99 MVCKECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 99 ~~C~~Cgk~F~~~~~L~~H~~~H~ 122 (527)
|.|++|++.|.+...|..|++.|.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHHS
T ss_pred CCCcCCCCcCCcHHHHHHHHHhhC
Confidence 789999999999999999998763
No 34
>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=97.22 E-value=0.0002 Score=41.26 Aligned_cols=24 Identities=38% Similarity=0.784 Sum_probs=20.4
Q ss_pred eecccCCCccCCchhHHHHhhhhc
Q 041528 11 FVCKYCNKRYPCGKSLGGHIRTHM 34 (527)
Q Consensus 11 ~~C~~C~k~f~~~~~L~~H~~~H~ 34 (527)
|.|++|++.|.+...|.+|++.|+
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 789999999999999999998874
No 35
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.09 E-value=0.00017 Score=42.32 Aligned_cols=25 Identities=48% Similarity=0.788 Sum_probs=22.9
Q ss_pred ccCCCcCccccchhhhccccccccc
Q 041528 461 HECPFCFRVFKSGQALGGHKRSHFV 485 (527)
Q Consensus 461 ~~C~iC~k~F~~~~~L~~H~r~H~~ 485 (527)
|.|+.|+++|.+...|..|++.|..
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~~ 25 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHXX 25 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhcc
Confidence 6899999999999999999998864
No 36
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=96.81 E-value=0.001 Score=44.98 Aligned_cols=34 Identities=26% Similarity=0.436 Sum_probs=24.0
Q ss_pred cCCCccccccccccccChhhHHHHHhhhcCCCCC
Q 041528 94 TSQQEMVCKECGKVFQSLKALCGHMACHSEKDNK 127 (527)
Q Consensus 94 ~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~ 127 (527)
..+.|-.|++|+..+.+..||++|+..+++.++.
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~~ 53 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKPG 53 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS--
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccCC
Confidence 3577889999999999999999999888877653
No 37
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.71 E-value=0.0011 Score=38.77 Aligned_cols=24 Identities=54% Similarity=0.893 Sum_probs=22.5
Q ss_pred cccccccccccChhhHHHHHhhhc
Q 041528 99 MVCKECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 99 ~~C~~Cgk~F~~~~~L~~H~~~H~ 122 (527)
|+|+.|++.|.....|..|++.|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 689999999999999999999876
No 38
>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=96.66 E-value=0.0014 Score=44.34 Aligned_cols=33 Identities=15% Similarity=0.266 Sum_probs=24.3
Q ss_pred cCCCceecccCCCccCCchhHHHHhhhhcCCCC
Q 041528 6 QKKKLFVCKYCNKRYPCGKSLGGHIRTHMNNGN 38 (527)
Q Consensus 6 ~~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~p 38 (527)
..+.|..|++|+..+....+|++|+.++++.+|
T Consensus 20 ~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp TTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred ccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 357899999999999999999999998888776
No 39
>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=96.57 E-value=0.0015 Score=46.34 Aligned_cols=49 Identities=16% Similarity=0.272 Sum_probs=34.6
Q ss_pred ccccccCCCccccCCCCCcccccchhhhh-ccCC-CccccccccccccChhhHHHHHhhhc
Q 041528 64 DSCFEAGGQSGYVLRANPKRTRRFVDSNT-LTSQ-QEMVCKECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 64 ~~c~~c~~~~~~~c~~c~~~~~~~~H~~~-h~~~-k~~~C~~Cgk~F~~~~~L~~H~~~H~ 122 (527)
|.|++|++.|.. ..|..|... |..+ +.+.|++|...+. .+|..|++.++
T Consensus 3 f~CP~C~~~~~~--------~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGKGFSE--------SSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCCccCH--------HHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 566777664432 256678665 6654 5799999999766 49999997764
No 40
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.52 E-value=0.00082 Score=40.05 Aligned_cols=23 Identities=39% Similarity=0.654 Sum_probs=21.5
Q ss_pred cccccccccccCccccccccccC
Q 041528 377 FKCLTCNKVFHSPRSLWGHTASH 399 (527)
Q Consensus 377 ~~C~~Cgk~F~~~~~L~~H~~~H 399 (527)
|.|.+|++.|.+...|..|++++
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 78999999999999999999873
No 41
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.51 E-value=0.00052 Score=40.06 Aligned_cols=23 Identities=35% Similarity=0.621 Sum_probs=21.4
Q ss_pred ccCCCcCccccchhhhccccccc
Q 041528 461 HECPFCFRVFKSGQALGGHKRSH 483 (527)
Q Consensus 461 ~~C~iC~k~F~~~~~L~~H~r~H 483 (527)
|.|++|++.|.+...|+.|++.|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 67999999999999999999875
No 42
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.47 E-value=0.00045 Score=40.32 Aligned_cols=23 Identities=48% Similarity=0.704 Sum_probs=21.5
Q ss_pred cccccccccccCccccccccccC
Q 041528 377 FKCLTCNKVFHSPRSLWGHTASH 399 (527)
Q Consensus 377 ~~C~~Cgk~F~~~~~L~~H~~~H 399 (527)
|.|++|++.|.+...|..|++.+
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcC
Confidence 68999999999999999999875
No 43
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.29 E-value=0.0019 Score=38.46 Aligned_cols=23 Identities=30% Similarity=0.512 Sum_probs=21.3
Q ss_pred ccCCCcCccccchhhhccccccc
Q 041528 461 HECPFCFRVFKSGQALGGHKRSH 483 (527)
Q Consensus 461 ~~C~iC~k~F~~~~~L~~H~r~H 483 (527)
|-|.+|++.|.+...|..||+.+
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSH
T ss_pred CCcccCCCCcCCHHHHHHHHccC
Confidence 78999999999999999999863
No 44
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=96.26 E-value=0.0025 Score=51.47 Aligned_cols=73 Identities=19% Similarity=0.367 Sum_probs=22.3
Q ss_pred ecccCCCccCCchhHHHHhhhhcCC-CCccccccccccccccccccccCCcccccccccCCCccccCCCCCcccccchhh
Q 041528 12 VCKYCNKRYPCGKSLGGHIRTHMNN-GNSAEAEGEGEVKLNIDKIFSGRNIKKDSCFEAGGQSGYVLRANPKRTRRFVDS 90 (527)
Q Consensus 12 ~C~~C~k~f~~~~~L~~H~~~H~~~-~p~~~C~~C~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~c~~c~~~~~~~~H~ 90 (527)
+|.+|+..|.....|..|+...++- .+- .. ....-. .+..+.
T Consensus 1 ~C~~C~~~f~~~~~l~~H~~~~H~~~~~~--~~---------------------~l~~~~--------------~~~~~~ 43 (100)
T PF12756_consen 1 QCLFCDESFSSVDDLLQHMKKKHGFDIPD--QK---------------------YLVDPN--------------RLLNYL 43 (100)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Ccccccccccccccccccccccccccccc--cc---------------------cccccc--------------cccccc
Confidence 5999999999999999999754332 110 00 000000 111111
Q ss_pred hhccCCCccccccccccccChhhHHHHHhhhc
Q 041528 91 NTLTSQQEMVCKECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 91 ~~h~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~ 122 (527)
+. .....+.|.+|++.|.....|..||+.+.
T Consensus 44 ~~-~~~~~~~C~~C~~~f~s~~~l~~Hm~~~~ 74 (100)
T PF12756_consen 44 RK-KVKESFRCPYCNKTFRSREALQEHMRSKH 74 (100)
T ss_dssp ------SSEEBSSSS-EESSHHHHHHHHHHTT
T ss_pred cc-ccCCCCCCCccCCCCcCHHHHHHHHcCcc
Confidence 11 11226899999999999999999998654
No 45
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.32 E-value=0.011 Score=33.94 Aligned_cols=23 Identities=22% Similarity=0.379 Sum_probs=18.9
Q ss_pred cccccccccccChhhHHHHHhhhc
Q 041528 99 MVCKECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 99 ~~C~~Cgk~F~~~~~L~~H~~~H~ 122 (527)
|+|+.|..+.. ...|.+|++.|.
T Consensus 1 y~C~~C~y~t~-~~~l~~H~~~~H 23 (24)
T PF13909_consen 1 YKCPHCSYSTS-KSNLKRHLKRHH 23 (24)
T ss_dssp EE-SSSS-EES-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCC-HHHHHHHHHhhC
Confidence 78999999998 999999998865
No 46
>PRK04860 hypothetical protein; Provisional
Probab=94.90 E-value=0.0079 Score=52.92 Aligned_cols=23 Identities=13% Similarity=0.397 Sum_probs=18.1
Q ss_pred CccccccccccccCccccccccccCCC
Q 041528 375 SQFKCLTCNKVFHSPRSLWGHTASHSK 401 (527)
Q Consensus 375 ~~~~C~~Cgk~F~~~~~L~~H~~~H~~ 401 (527)
-+|.|. |++ ....+.+|.++|++
T Consensus 118 ~~Y~C~-C~~---~~~~~rrH~ri~~g 140 (160)
T PRK04860 118 FPYRCK-CQE---HQLTVRRHNRVVRG 140 (160)
T ss_pred EEEEcC-CCC---eeCHHHHHHHHhcC
Confidence 469998 988 77777888877776
No 47
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=94.76 E-value=0.018 Score=33.04 Aligned_cols=24 Identities=21% Similarity=0.523 Sum_probs=19.2
Q ss_pred eecccCCCccCCchhHHHHhhhhcC
Q 041528 11 FVCKYCNKRYPCGKSLGGHIRTHMN 35 (527)
Q Consensus 11 ~~C~~C~k~f~~~~~L~~H~~~H~~ 35 (527)
|+|..|+...+ ...|.+|++.|++
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 78999999988 8999999998653
No 48
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=94.25 E-value=0.015 Score=33.75 Aligned_cols=21 Identities=33% Similarity=0.694 Sum_probs=17.5
Q ss_pred ccCCCcCccccchhhhcccccc
Q 041528 461 HECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 461 ~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
..|++||+.| ...+|.+|+++
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 4699999999 77889999764
No 49
>PRK04860 hypothetical protein; Provisional
Probab=93.71 E-value=0.03 Score=49.34 Aligned_cols=42 Identities=12% Similarity=0.229 Sum_probs=31.7
Q ss_pred CCCccccCCCCCcc-cccchhhhhccCCCccccccccccccChh
Q 041528 70 GGQSGYVLRANPKR-TRRFVDSNTLTSQQEMVCKECGKVFQSLK 112 (527)
Q Consensus 70 ~~~~~~~c~~c~~~-~~~~~H~~~h~~~k~~~C~~Cgk~F~~~~ 112 (527)
++.|+|.|. |+.. ..+..|.++|+++++|.|..|+..|....
T Consensus 115 ~~~~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~ 157 (160)
T PRK04860 115 GKTFPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFKG 157 (160)
T ss_pred cCEEEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEec
Confidence 345677776 7642 23456999999999999999999987653
No 50
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=93.01 E-value=0.027 Score=35.70 Aligned_cols=24 Identities=29% Similarity=0.490 Sum_probs=21.6
Q ss_pred CccccccccccccCcccccccccc
Q 041528 375 SQFKCLTCNKVFHSPRSLWGHTAS 398 (527)
Q Consensus 375 ~~~~C~~Cgk~F~~~~~L~~H~~~ 398 (527)
.+|.|++|++.|.+..+|..|++.
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHCh
Confidence 468899999999999999999865
No 51
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=92.78 E-value=0.04 Score=34.87 Aligned_cols=23 Identities=22% Similarity=0.546 Sum_probs=21.0
Q ss_pred CccCCCcCccccchhhhcccccc
Q 041528 460 GHECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 460 p~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
+|.|++|++.|.+...+..|++.
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~g 25 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKG 25 (35)
T ss_pred CeEccccCCccCCHHHHHHHHCh
Confidence 58899999999999999999875
No 52
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=92.19 E-value=0.11 Score=30.25 Aligned_cols=21 Identities=29% Similarity=0.556 Sum_probs=17.4
Q ss_pred cccccccccccChhhHHHHHhh
Q 041528 99 MVCKECGKVFQSLKALCGHMAC 120 (527)
Q Consensus 99 ~~C~~Cgk~F~~~~~L~~H~~~ 120 (527)
..|++||+.| ....|..|+.+
T Consensus 3 ~~C~~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 3 VPCPICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred CcCCCCCCEE-CHHHHHHHHHh
Confidence 3699999999 67788999864
No 53
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=92.12 E-value=0.04 Score=50.11 Aligned_cols=47 Identities=19% Similarity=0.243 Sum_probs=37.8
Q ss_pred cccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhccc-cccccc
Q 041528 433 KSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGH-KRSHFV 485 (527)
Q Consensus 433 c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H-~r~H~~ 485 (527)
|=+|+.-| .... ....|.+.|-|+|.||.|..-+.-.|..| |..|..
T Consensus 13 cwycnref--ddek----iliqhqkakhfkchichkkl~sgpglsihcmqvhke 60 (341)
T KOG2893|consen 13 CWYCNREF--DDEK----ILIQHQKAKHFKCHICHKKLFSGPGLSIHCMQVHKE 60 (341)
T ss_pred eeeccccc--chhh----hhhhhhhhccceeeeehhhhccCCCceeehhhhhhh
Confidence 67888888 4443 44455667999999999999999999999 888864
No 54
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=91.73 E-value=0.12 Score=53.74 Aligned_cols=58 Identities=17% Similarity=0.153 Sum_probs=51.6
Q ss_pred CCcccccCCCCcccccCcccccccc--ccCCC--CCccCC--CcCccccchhhhcccccccccCCC
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRL--GSKKS--KGHECP--FCFRVFKSGQALGGHKRSHFVGGS 488 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~--~Ht~e--kp~~C~--iC~k~F~~~~~L~~H~r~H~~~~~ 488 (527)
..+.|..|...| .....+..|.+ .|+++ +||.|+ .|++.|.+...|.+|..+|++-..
T Consensus 288 ~~~~~~~~~~~~--s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (467)
T COG5048 288 LPIKSKQCNISF--SRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISP 351 (467)
T ss_pred cCCCCccccCCc--cccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCc
Confidence 356678899999 89999999999 89999 999999 899999999999999999987553
No 55
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.37 E-value=0.082 Score=59.88 Aligned_cols=79 Identities=22% Similarity=0.219 Sum_probs=53.2
Q ss_pred CccccccccccccCcccccccccc-CCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCcccccccc
Q 041528 375 SQFKCLTCNKVFHSPRSLWGHTAS-HSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKRL 453 (527)
Q Consensus 375 ~~~~C~~Cgk~F~~~~~L~~H~~~-H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~~ 453 (527)
+.|.|..|+..|+....|..|||+ |..... -.|... ++.-.+..-..
T Consensus 464 kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~-~~c~~g-------------------------------q~~~~~arg~~ 511 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQTLGVHMRSKHPESQS-AYCKAG-------------------------------QNHPRLARGEV 511 (1406)
T ss_pred ccccCCccchhhhhHHHhhhcccccccccch-hHhHhc-------------------------------ccccccccccc
Confidence 889999999999999999999998 433221 111111 11111111111
Q ss_pred ccCCCCCccCCCcCccccchhhhcccccc--ccc
Q 041528 454 GSKKSKGHECPFCFRVFKSGQALGGHKRS--HFV 485 (527)
Q Consensus 454 ~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~--H~~ 485 (527)
.--+-+||.|..|...|+++.+|-+||.. |..
T Consensus 512 ~~~~~~p~~C~~C~~stttng~LsihlqS~~h~~ 545 (1406)
T KOG1146|consen 512 YRCPGKPYPCRACNYSTTTNGNLSIHLQSDLHRN 545 (1406)
T ss_pred ccCCCCcccceeeeeeeecchHHHHHHHHHhhHH
Confidence 22346899999999999999999999874 543
No 56
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.81 E-value=0.045 Score=58.39 Aligned_cols=98 Identities=17% Similarity=0.144 Sum_probs=50.7
Q ss_pred cccccccccCccccccccccCCCCCCCCccccc---cc----------CCCcCcCCCCCC-CCCCCcccccCCCCccccc
Q 041528 379 CLTCNKVFHSPRSLWGHTASHSKINGCCESINE---SS----------ENSRETDSFPVP-MPNSKFCKSVNGKTPIAQN 444 (527)
Q Consensus 379 C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~---f~----------~~~~~~~~~~~~-~~~~~~~c~~C~K~f~~~~ 444 (527)
|..| -.|.+...|+.||+.=++...|..|... |. ...++..-.+.. ....--.|..|...| -.
T Consensus 118 ~~~c-~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~f--ld 194 (669)
T KOG2231|consen 118 CLHC-TEFKSVENLKNHMRDQHKLHLCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERF--LD 194 (669)
T ss_pred Cccc-cchhHHHHHHHHHHHhhhhhccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhh--cc
Confidence 3333 3344888999999554434445544332 21 011111111210 111123477777777 45
Q ss_pred CccccccccccCCCCCccCCCcC------ccccchhhhccccccc
Q 041528 445 LSTNVDKRLGSKKSKGHECPFCF------RVFKSGQALGGHKRSH 483 (527)
Q Consensus 445 ~~~l~~h~~~Ht~ekp~~C~iC~------k~F~~~~~L~~H~r~H 483 (527)
...|.+|++. .-|.|.+|. --|....-|..|.|.+
T Consensus 195 ~~el~rH~~~----~h~~chfC~~~~~~neyy~~~~dLe~HfR~~ 235 (669)
T KOG2231|consen 195 DDELYRHLRF----DHEFCHFCDYKTGQNEYYNDYDDLEEHFRKG 235 (669)
T ss_pred HHHHHHhhcc----ceeheeecCcccccchhcccchHHHHHhhhc
Confidence 5556666553 236677773 4456777788887664
No 57
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=90.63 E-value=0.41 Score=49.59 Aligned_cols=51 Identities=16% Similarity=0.062 Sum_probs=37.6
Q ss_pred CCCCcccccCccccccccccCCCC--CccCCCcCccccchhhhcccccccccCCC
Q 041528 436 NGKTPIAQNLSTNVDKRLGSKKSK--GHECPFCFRVFKSGQALGGHKRSHFVGGS 488 (527)
Q Consensus 436 C~K~f~~~~~~~l~~h~~~Ht~ek--p~~C~iC~k~F~~~~~L~~H~r~H~~~~~ 488 (527)
|...+ .....+..|...|.... .+.+..|.+.|.....|..|++.|.....
T Consensus 394 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 446 (467)
T COG5048 394 CIRNF--KRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHTNHAP 446 (467)
T ss_pred hhhhh--ccccccccccccccccCCcCCCCCcchhhccCcccccccccccccCCc
Confidence 44444 56666666666666555 77889999999999999999999876543
No 58
>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=89.70 E-value=0.31 Score=39.79 Aligned_cols=32 Identities=19% Similarity=0.152 Sum_probs=25.4
Q ss_pred CCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccch
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSG 473 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~ 473 (527)
....|+.||++| -=.+..|-.|+.||..|.-.
T Consensus 8 tKR~Cp~CG~kF-------------YDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKF-------------YDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchh-------------ccCCCCCccCCCCCCccCcc
Confidence 345699999999 23445789999999999876
No 59
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.40 E-value=0.31 Score=34.45 Aligned_cols=34 Identities=24% Similarity=0.353 Sum_probs=24.5
Q ss_pred cccccccccCCCccccCCCCCcccccchhhhhccCCCccccccccc
Q 041528 61 IKKDSCFEAGGQSGYVLRANPKRTRRFVDSNTLTSQQEMVCKECGK 106 (527)
Q Consensus 61 ~~~~~c~~c~~~~~~~c~~c~~~~~~~~H~~~h~~~k~~~C~~Cgk 106 (527)
...|.|..||....+.|..|.+.. .+|.|+.||.
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~------------~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQS------------NPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcC------------CceECCCCCC
Confidence 456788888877677777775333 3799999985
No 60
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=86.07 E-value=0.13 Score=58.29 Aligned_cols=93 Identities=13% Similarity=0.081 Sum_probs=56.2
Q ss_pred CCccccccccccccCccccccccccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCcccccccc
Q 041528 374 RSQFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKRL 453 (527)
Q Consensus 374 ~~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~~ 453 (527)
.+.+.|..|.+.|...-.+. |+-+-. .+.|..|...|.-.+.+..|. ..|.+.| ......--+.+
T Consensus 1258 sGe~~c~~~~~~~~~~~~~~-~l~~~~-~~~~~~~~~~~~~~~~l~~~~-----------~k~~~~~--~~~~~~~~~~l 1322 (1406)
T KOG1146|consen 1258 SGEGECGAVDELLTPSFGIS-TLDVTH-RYLCRQCKMAFDGEAPLTAHQ-----------RKFCFAG--RGSGGSMPPPL 1322 (1406)
T ss_pred CCcchhhhccccccCcccee-ecccch-hHHHHHHHhhhcchhHHHHHH-----------HHHHhcc--CccccCCCCcc
Confidence 34555555555555555555 432211 134555555554444443332 1223333 44445555677
Q ss_pred ccCCCCCccCCCcCccccchhhhcccccc
Q 041528 454 GSKKSKGHECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 454 ~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
.|...++| |.+|...|.....|..|||+
T Consensus 1323 ~~~d~~~~-c~~c~~~~~~~~alqihm~~ 1350 (1406)
T KOG1146|consen 1323 RVPDCTYH-CLACEVLLSGREALQIHMRS 1350 (1406)
T ss_pred cCcccccc-chHHHhhcchhHHHHHHHHH
Confidence 77778889 99999999999999999997
No 61
>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=85.73 E-value=0.75 Score=38.15 Aligned_cols=36 Identities=17% Similarity=0.110 Sum_probs=28.1
Q ss_pred CCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhc
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALG 477 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~ 477 (527)
.+..|+.||++| .-.+..|-.|+.||..|.-...++
T Consensus 8 tKr~Cp~cg~kF-------------YDLnk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 8 TKRICPNTGSKF-------------YDLNRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred ccccCCCcCccc-------------cccCCCCccCCCcCCccCcchhhc
Confidence 445699999999 244568999999999997765555
No 62
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.00 E-value=0.46 Score=50.94 Aligned_cols=101 Identities=12% Similarity=0.112 Sum_probs=53.2
Q ss_pred CccCCchhHHHHhh-hhcCCCCcccccccccc---ccccccccccCCccccccc--ccCCCc--cccCCCCCcccccchh
Q 041528 18 KRYPCGKSLGGHIR-THMNNGNSAEAEGEGEV---KLNIDKIFSGRNIKKDSCF--EAGGQS--GYVLRANPKRTRRFVD 89 (527)
Q Consensus 18 k~f~~~~~L~~H~~-~H~~~~p~~~C~~C~~~---~~~~~~~~~~~~~~~~~c~--~c~~~~--~~~c~~c~~~~~~~~H 89 (527)
-.|..-..|++|++ .|. .+ .|.+|... |....+.|+...+..+.-. .++..+ --.|..|...|.-..-
T Consensus 122 ~~~~s~~~Lk~H~~~~H~---~~-~c~lC~~~~kif~~e~k~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~e 197 (669)
T KOG2231|consen 122 TEFKSVENLKNHMRDQHK---LH-LCSLCLQNLKIFINERKLYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDE 197 (669)
T ss_pred cchhHHHHHHHHHHHhhh---hh-ccccccccceeeeeeeehehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHH
Confidence 33346778999995 563 34 88888542 2222444443322111111 012222 1245555544433333
Q ss_pred hhhccCCCccccccc------cccccChhhHHHHHhhhc
Q 041528 90 SNTLTSQQEMVCKEC------GKVFQSLKALCGHMACHS 122 (527)
Q Consensus 90 ~~~h~~~k~~~C~~C------gk~F~~~~~L~~H~~~H~ 122 (527)
+..|....-|.|.+| +.-|.....|..|.|.++
T Consensus 198 l~rH~~~~h~~chfC~~~~~~neyy~~~~dLe~HfR~~H 236 (669)
T KOG2231|consen 198 LYRHLRFDHEFCHFCDYKTGQNEYYNDYDDLEEHFRKGH 236 (669)
T ss_pred HHHhhccceeheeecCcccccchhcccchHHHHHhhhcC
Confidence 333444445677777 355777788888887766
No 63
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.63 E-value=0.42 Score=33.72 Aligned_cols=38 Identities=24% Similarity=0.344 Sum_probs=26.3
Q ss_pred ccCCcccccccccCCCccccCCCCCcccccchhhhhccCCCccccccccc
Q 041528 57 SGRNIKKDSCFEAGGQSGYVLRANPKRTRRFVDSNTLTSQQEMVCKECGK 106 (527)
Q Consensus 57 ~~~~~~~~~c~~c~~~~~~~c~~c~~~~~~~~H~~~h~~~k~~~C~~Cgk 106 (527)
.+.....|.|..||....+.|..|.+. ..+|.|+-||.
T Consensus 21 p~e~~v~F~CPnCGe~~I~Rc~~CRk~------------g~~Y~Cp~CGF 58 (61)
T COG2888 21 PGETAVKFPCPNCGEVEIYRCAKCRKL------------GNPYRCPKCGF 58 (61)
T ss_pred cCCceeEeeCCCCCceeeehhhhHHHc------------CCceECCCcCc
Confidence 334445678888888888888766522 23899999984
No 64
>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=83.60 E-value=0.76 Score=28.65 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=17.9
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCcc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRV 469 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~ 469 (527)
|.|..||-.+. ..+.++.|++||..
T Consensus 2 ~~C~~CGy~y~--------------~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYD--------------GEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEEC--------------CCcCCCcCcCCCCc
Confidence 56788887762 22379999999863
No 65
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=79.64 E-value=0.77 Score=31.78 Aligned_cols=29 Identities=14% Similarity=0.352 Sum_probs=25.6
Q ss_pred cccCCCceecccCCCccCCchhHHHHhhh
Q 041528 4 ANQKKKLFVCKYCNKRYPCGKSLGGHIRT 32 (527)
Q Consensus 4 ~h~~~~~~~C~~C~k~f~~~~~L~~H~~~ 32 (527)
...|+.-+.|+-|++.|.......+|+..
T Consensus 11 ~RDGE~~lrCPRC~~~FR~~K~Y~RHVNK 39 (65)
T COG4049 11 DRDGEEFLRCPRCGMVFRRRKDYIRHVNK 39 (65)
T ss_pred ccCCceeeeCCchhHHHHHhHHHHHHhhH
Confidence 45678889999999999999999999964
No 66
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=78.88 E-value=0.63 Score=32.22 Aligned_cols=34 Identities=21% Similarity=0.215 Sum_probs=28.4
Q ss_pred ccccCCCCCccCCCcCccccchhhhccccc-cccc
Q 041528 452 RLGSKKSKGHECPFCFRVFKSGQALGGHKR-SHFV 485 (527)
Q Consensus 452 ~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r-~H~~ 485 (527)
.+.-.||--++|+-||+.|.......+|.. .|.+
T Consensus 9 v~~RDGE~~lrCPRC~~~FR~~K~Y~RHVNKaH~~ 43 (65)
T COG4049 9 VRDRDGEEFLRCPRCGMVFRRRKDYIRHVNKAHGW 43 (65)
T ss_pred eeccCCceeeeCCchhHHHHHhHHHHHHhhHHhhh
Confidence 445678899999999999999999999976 4644
No 67
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=78.00 E-value=0.79 Score=31.68 Aligned_cols=25 Identities=24% Similarity=0.519 Sum_probs=19.0
Q ss_pred ccCCCcCccccch-----hhhccccc-cccc
Q 041528 461 HECPFCFRVFKSG-----QALGGHKR-SHFV 485 (527)
Q Consensus 461 ~~C~iC~k~F~~~-----~~L~~H~r-~H~~ 485 (527)
=.|..|++.+... ++|.+|++ +|..
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~ 49 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLRRKHPA 49 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHHhHCcC
Confidence 4588888888654 69999988 6754
No 68
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.29 E-value=1.6 Score=34.94 Aligned_cols=30 Identities=10% Similarity=0.053 Sum_probs=23.7
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCccccch
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSG 473 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~ 473 (527)
-+|+.||++| .-....|-.|++||+.|..+
T Consensus 10 ridPetg~KF-------------YDLNrdPiVsPytG~s~P~s 39 (129)
T COG4530 10 RIDPETGKKF-------------YDLNRDPIVSPYTGKSYPRS 39 (129)
T ss_pred ccCccccchh-------------hccCCCccccCcccccchHH
Confidence 3588999999 24457899999999999543
No 69
>PF14353 CpXC: CpXC protein
Probab=76.07 E-value=1.3 Score=37.53 Aligned_cols=23 Identities=26% Similarity=0.414 Sum_probs=19.9
Q ss_pred CccCCCcCccccchhhhcccccc
Q 041528 460 GHECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 460 p~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
.|.|+.||..|.-...+..|-..
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCC
Confidence 69999999999999999888444
No 70
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=75.53 E-value=1.9 Score=29.75 Aligned_cols=24 Identities=33% Similarity=0.587 Sum_probs=19.1
Q ss_pred ccccccccccCh-----hhHHHHHh-hhcC
Q 041528 100 VCKECGKVFQSL-----KALCGHMA-CHSE 123 (527)
Q Consensus 100 ~C~~Cgk~F~~~-----~~L~~H~~-~H~~ 123 (527)
.|..|++.+... ++|.+|++ .|+.
T Consensus 20 ~C~~C~~~l~~~~~~gTs~L~rHl~~~h~~ 49 (50)
T smart00614 20 KCKYCGKKLSRSSKGGTSNLRRHLRRKHPA 49 (50)
T ss_pred EecCCCCEeeeCCCCCcHHHHHHHHhHCcC
Confidence 588888888776 59999997 6763
No 71
>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=75.21 E-value=1.9 Score=28.90 Aligned_cols=27 Identities=33% Similarity=0.607 Sum_probs=17.6
Q ss_pred CCCccccccccccccCh----hhHHHHH-hhh
Q 041528 95 SQQEMVCKECGKVFQSL----KALCGHM-ACH 121 (527)
Q Consensus 95 ~~k~~~C~~Cgk~F~~~----~~L~~H~-~~H 121 (527)
+.....|.+|++.|... ++|.+|+ +.|
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~~~h 44 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLKKKH 44 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHHHTT
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhhhhC
Confidence 34556799999999875 7999999 555
No 72
>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=74.99 E-value=1.9 Score=27.10 Aligned_cols=23 Identities=22% Similarity=0.455 Sum_probs=17.0
Q ss_pred cccccCCCCcccccCccccccccccCC-CCCccCCCcCc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKK-SKGHECPFCFR 468 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~-ekp~~C~iC~k 468 (527)
|.|..||-.+ .+ +.|-.|++||.
T Consensus 3 ~~C~~CG~i~---------------~g~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIH---------------EGEEAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEe---------------ECCcCCCcCcCCCC
Confidence 5688888665 23 36889999986
No 73
>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=74.84 E-value=1.3 Score=25.98 Aligned_cols=20 Identities=30% Similarity=0.777 Sum_probs=15.8
Q ss_pred ccCCCcCccccchhhhccccc
Q 041528 461 HECPFCFRVFKSGQALGGHKR 481 (527)
Q Consensus 461 ~~C~iC~k~F~~~~~L~~H~r 481 (527)
..||||++.+ ....+..|+.
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 3699999999 6677777764
No 74
>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=74.05 E-value=2.3 Score=28.46 Aligned_cols=25 Identities=36% Similarity=0.659 Sum_probs=17.0
Q ss_pred CCCceecccCCCccCCc----hhHHHHhh
Q 041528 7 KKKLFVCKYCNKRYPCG----KSLGGHIR 31 (527)
Q Consensus 7 ~~~~~~C~~C~k~f~~~----~~L~~H~~ 31 (527)
++...+|.+|++.+... +.|.+|++
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45678899999999885 78999994
No 75
>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=72.92 E-value=2.8 Score=24.58 Aligned_cols=14 Identities=29% Similarity=0.626 Sum_probs=9.2
Q ss_pred CCCccCCCcCcccc
Q 041528 458 SKGHECPFCFRVFK 471 (527)
Q Consensus 458 ekp~~C~iC~k~F~ 471 (527)
...-.|+.||..|.
T Consensus 12 ~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 12 ESAKFCPHCGYDFE 25 (26)
T ss_pred hhcCcCCCCCCCCc
Confidence 33456888887774
No 76
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=72.79 E-value=2.2 Score=39.11 Aligned_cols=40 Identities=28% Similarity=0.443 Sum_probs=31.6
Q ss_pred eecccCCCccCCchhHHHHhhhhcCCCCccccccccccccccccccccCCc
Q 041528 11 FVCKYCNKRYPCGKSLGGHIRTHMNNGNSAEAEGEGEVKLNIDKIFSGRNI 61 (527)
Q Consensus 11 ~~C~~C~k~f~~~~~L~~H~~~H~~~~p~~~C~~C~~~~~~~~~~~~~~~~ 61 (527)
=.|=+|++.|-...-|++|++.- -| +|.+|.| +.|++..+
T Consensus 11 pwcwycnrefddekiliqhqkak----hf-kchichk------kl~sgpgl 50 (341)
T KOG2893|consen 11 PWCWYCNREFDDEKILIQHQKAK----HF-KCHICHK------KLFSGPGL 50 (341)
T ss_pred ceeeecccccchhhhhhhhhhhc----cc-eeeeehh------hhccCCCc
Confidence 35999999999999999998752 25 9999975 56666654
No 77
>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=70.63 E-value=2.1 Score=36.29 Aligned_cols=27 Identities=30% Similarity=0.631 Sum_probs=18.1
Q ss_pred CceecccCCCccCCchhHHHHhhhhcCCCC
Q 041528 9 KLFVCKYCNKRYPCGKSLGGHIRTHMNNGN 38 (527)
Q Consensus 9 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~p 38 (527)
.--.|-.|||.|+. |++|++.|+|-.|
T Consensus 71 d~i~clecGk~~k~---LkrHL~~~~gltp 97 (132)
T PF05443_consen 71 DYIICLECGKKFKT---LKRHLRTHHGLTP 97 (132)
T ss_dssp S-EE-TBT--EESB---HHHHHHHTT-S-H
T ss_pred CeeEEccCCcccch---HHHHHHHccCCCH
Confidence 44679999999986 7999999988766
No 78
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=70.01 E-value=2.8 Score=36.99 Aligned_cols=22 Identities=27% Similarity=0.484 Sum_probs=17.3
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcC
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCF 467 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~ 467 (527)
|.|..||-.+ -|+-|-.||+||
T Consensus 135 ~vC~vCGy~~---------------~ge~P~~CPiCg 156 (166)
T COG1592 135 WVCPVCGYTH---------------EGEAPEVCPICG 156 (166)
T ss_pred EEcCCCCCcc---------------cCCCCCcCCCCC
Confidence 5566776665 579999999999
No 79
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=69.59 E-value=0.5 Score=50.30 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=25.8
Q ss_pred CCccCCCcCccccchhhhcccccccccCC
Q 041528 459 KGHECPFCFRVFKSGQALGGHKRSHFVGG 487 (527)
Q Consensus 459 kp~~C~iC~k~F~~~~~L~~H~r~H~~~~ 487 (527)
--|.|..|+|.|..-.++..||++|.-..
T Consensus 791 giFpCreC~kvF~KiKSrNAHMK~Hr~q~ 819 (907)
T KOG4167|consen 791 GIFPCRECGKVFFKIKSRNAHMKTHRQQE 819 (907)
T ss_pred ceeehHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 46999999999999999999999997544
No 80
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=66.70 E-value=3.3 Score=36.24 Aligned_cols=21 Identities=19% Similarity=0.249 Sum_probs=15.7
Q ss_pred CccCCCcCccccchhhhcccc
Q 041528 460 GHECPFCFRVFKSGQALGGHK 480 (527)
Q Consensus 460 p~~C~iC~k~F~~~~~L~~H~ 480 (527)
.++|+-||+.|.+.-.+..=|
T Consensus 28 ~~~c~~c~~~f~~~e~~~~~~ 48 (154)
T PRK00464 28 RRECLACGKRFTTFERVELVP 48 (154)
T ss_pred eeeccccCCcceEeEeccCcc
Confidence 388999999998766555444
No 81
>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=65.91 E-value=3.9 Score=27.05 Aligned_cols=29 Identities=17% Similarity=0.102 Sum_probs=18.3
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFR 468 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k 468 (527)
|.|..||..|- ..+.+.. ..+-.|+.||.
T Consensus 6 y~C~~Cg~~fe--------~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFE--------VLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEE--------EEEEcCC-CCCCcCCCCCC
Confidence 55778887772 2222333 56778888887
No 82
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=65.29 E-value=3.8 Score=27.69 Aligned_cols=30 Identities=17% Similarity=0.339 Sum_probs=19.0
Q ss_pred CcccccCCCCcccccCccccccccccCCCCCccCCCcCcccc
Q 041528 430 KFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFK 471 (527)
Q Consensus 430 ~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~ 471 (527)
.|.|+.||..|. . -.....+.|+.||-.+.
T Consensus 3 ~y~C~~CG~~~~--~----------~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVE--L----------DEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEE--E----------CCCCCceECCCCCCeEE
Confidence 356788888772 0 11112688999997664
No 83
>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=65.24 E-value=3.4 Score=28.68 Aligned_cols=30 Identities=17% Similarity=0.505 Sum_probs=19.0
Q ss_pred ccccccccccccCccccccccccCCCCCCCCcccc
Q 041528 376 QFKCLTCNKVFHSPRSLWGHTASHSKINGCCESIN 410 (527)
Q Consensus 376 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~ 410 (527)
-|.|..||..|.-...+.. .....|+.|+-
T Consensus 5 ey~C~~Cg~~fe~~~~~~~-----~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSD-----DPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCC-----CCCCCCCCCCC
Confidence 4889999999985533221 23346776654
No 84
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=65.03 E-value=6.2 Score=37.86 Aligned_cols=49 Identities=24% Similarity=0.245 Sum_probs=33.1
Q ss_pred ccccccCCCccccCCCCCcccccchhhhh-ccCCCccccccccccccChhhHHHHHhhhc
Q 041528 64 DSCFEAGGQSGYVLRANPKRTRRFVDSNT-LTSQQEMVCKECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 64 ~~c~~c~~~~~~~c~~c~~~~~~~~H~~~-h~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~ 122 (527)
-+|..|...|+- +..|--- -+..-.|+|+.|...|...-+.-.|-..|-
T Consensus 363 ~~Cf~CQ~~fp~----------~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~ 412 (421)
T COG5151 363 THCFVCQGPFPK----------PPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHF 412 (421)
T ss_pred ccceeccCCCCC----------CCCCcccccccccceechhhhhhhhhhhHHHHHHHHhh
Confidence 367778777764 2222111 123346999999999999999888887775
No 85
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=64.68 E-value=2.1 Score=38.49 Aligned_cols=78 Identities=19% Similarity=0.231 Sum_probs=49.6
Q ss_pred ceeccc--CCCccCCchhHHHHhhhhcCCCCccccccccccccccccccccCCcccccccccCCCccccCCCCCcccccc
Q 041528 10 LFVCKY--CNKRYPCGKSLGGHIRTHMNNGNSAEAEGEGEVKLNIDKIFSGRNIKKDSCFEAGGQSGYVLRANPKRTRRF 87 (527)
Q Consensus 10 ~~~C~~--C~k~f~~~~~L~~H~~~H~~~~p~~~C~~C~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~c~~c~~~~~~~ 87 (527)
.|.|++ |...|..-.....|..+-++. .|.+|.+.|+.. ..|-
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~----------------------------sCs~C~r~~Pt~-------hLLd 123 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN----------------------------SCSFCKRAFPTG-------HLLD 123 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc----------------------------hhHHHHHhCCch-------hhhh
Confidence 356665 667777766666776543333 455566666542 1222
Q ss_pred hhhhh-c---------cCCCcccccc--ccccccChhhHHHHH-hhhc
Q 041528 88 VDSNT-L---------TSQQEMVCKE--CGKVFQSLKALCGHM-ACHS 122 (527)
Q Consensus 88 ~H~~~-h---------~~~k~~~C~~--Cgk~F~~~~~L~~H~-~~H~ 122 (527)
.|..- | .|.--|+|=+ |+..|.+...-+.|+ ++|.
T Consensus 124 ~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk 171 (253)
T KOG4173|consen 124 AHILEWHDSLFQALVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMHK 171 (253)
T ss_pred HHHHHHHHHHHHHHHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhcc
Confidence 24311 2 3444589966 999999999999999 8886
No 86
>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=64.57 E-value=3.6 Score=26.80 Aligned_cols=30 Identities=17% Similarity=0.504 Sum_probs=18.7
Q ss_pred ccccccccccccCccccccccccCCCCCCCCcccc
Q 041528 376 QFKCLTCNKVFHSPRSLWGHTASHSKINGCCESIN 410 (527)
Q Consensus 376 ~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~ 410 (527)
.|.|..||+.|.-...... .....|+.|+.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~-----~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD-----DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCC-----CCCCCCCCCCC
Confidence 4889999998875554422 22336776554
No 87
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.56 E-value=14 Score=30.27 Aligned_cols=26 Identities=27% Similarity=0.418 Sum_probs=19.0
Q ss_pred CccccccccccccChhhHHHHHhhhc
Q 041528 97 QEMVCKECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 97 k~~~C~~Cgk~F~~~~~L~~H~~~H~ 122 (527)
-.|+|+.|...|--.-..-.|...|.
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESLHC 105 (112)
T ss_pred cceeCCCCCCccccccchhhhhhccC
Confidence 35778888888887777777776664
No 88
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=63.65 E-value=1.5 Score=42.52 Aligned_cols=102 Identities=22% Similarity=0.204 Sum_probs=62.0
Q ss_pred ccccc--ccccccCccccccccccCCCCCCCCccccccc---------CCCcCcCCCCC----CCCCCCcccccCCCCcc
Q 041528 377 FKCLT--CNKVFHSPRSLWGHTASHSKINGCCESINESS---------ENSRETDSFPV----PMPNSKFCKSVNGKTPI 441 (527)
Q Consensus 377 ~~C~~--Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~---------~~~~~~~~~~~----~~~~~~~~c~~C~K~f~ 441 (527)
|.|.. |..+-...-.|+.|.++-++..-|.+|...-. ....|..|... .+...--.|..|.+.|
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~~~~C~~C~~nKk~F~~E~~lF~~~~Lr~H~~~G~~e~GFKGHP~C~FC~~~F- 230 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHGFVLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYF- 230 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcCcEEhHhhhcCcccCccceeeeecccccccccCCccccCcCCCchhhhcccee-
Confidence 55553 55555557778888877666667777754322 22333333211 1223334588999999
Q ss_pred cccCccccccccccCCCCCccCCCcCcc-------ccchhhhccccc-ccc
Q 041528 442 AQNLSTNVDKRLGSKKSKGHECPFCFRV-------FKSGQALGGHKR-SHF 484 (527)
Q Consensus 442 ~~~~~~l~~h~~~Ht~ekp~~C~iC~k~-------F~~~~~L~~H~r-~H~ 484 (527)
-.--.|.+|+|. +-=+|.||++. |...-.|..|.+ .|.
T Consensus 231 -YdDDEL~~HcR~----~HE~ChICD~v~p~~~QYFK~Y~~Le~HF~~~hy 276 (493)
T COG5236 231 -YDDDELRRHCRL----RHEACHICDMVGPIRYQYFKSYEDLEAHFRNAHY 276 (493)
T ss_pred -cChHHHHHHHHh----hhhhhhhhhccCccchhhhhCHHHHHHHhhcCce
Confidence 666677777763 34458888765 677778888855 353
No 89
>PHA00626 hypothetical protein
Probab=61.13 E-value=5.1 Score=27.97 Aligned_cols=15 Identities=27% Similarity=0.501 Sum_probs=11.8
Q ss_pred ccccccccccccChh
Q 041528 98 EMVCKECGKVFQSLK 112 (527)
Q Consensus 98 ~~~C~~Cgk~F~~~~ 112 (527)
.|+|+.||..|....
T Consensus 23 rYkCkdCGY~ft~~~ 37 (59)
T PHA00626 23 DYVCCDCGYNDSKDA 37 (59)
T ss_pred ceEcCCCCCeechhh
Confidence 688888888887654
No 90
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=60.20 E-value=5.8 Score=25.77 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=12.1
Q ss_pred CccCCCcCccccchh
Q 041528 460 GHECPFCFRVFKSGQ 474 (527)
Q Consensus 460 p~~C~iC~k~F~~~~ 474 (527)
||+|..|++.|=...
T Consensus 12 ~f~C~~C~~~FC~~H 26 (39)
T smart00154 12 GFKCRHCGNLFCGEH 26 (39)
T ss_pred CeECCccCCcccccc
Confidence 899999999986544
No 91
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=60.15 E-value=1.4 Score=46.99 Aligned_cols=29 Identities=31% Similarity=0.571 Sum_probs=26.8
Q ss_pred cCCccccccccccccCccccccccccCCC
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWGHTASHSK 401 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~H~~~H~~ 401 (527)
..+.|.|..|+|+|-...++..||++|.-
T Consensus 789 ~~giFpCreC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 789 PTGIFPCRECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred CCceeehHHHHHHHHHHhhhhHHHHHHHH
Confidence 36899999999999999999999999983
No 92
>PF14353 CpXC: CpXC protein
Probab=60.02 E-value=3.9 Score=34.64 Aligned_cols=23 Identities=26% Similarity=0.443 Sum_probs=17.8
Q ss_pred ccccccccccccChhhHHHHHhh
Q 041528 98 EMVCKECGKVFQSLKALCGHMAC 120 (527)
Q Consensus 98 ~~~C~~Cgk~F~~~~~L~~H~~~ 120 (527)
.|.|+.||..|.-...+.-|-..
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCC
Confidence 48899999999887776666543
No 93
>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=58.41 E-value=6.9 Score=27.57 Aligned_cols=28 Identities=29% Similarity=0.348 Sum_probs=21.4
Q ss_pred ccccCCCCcccccCccccccccccCCCCCccCCCcCccccch
Q 041528 432 CKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSG 473 (527)
Q Consensus 432 ~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~ 473 (527)
.|..|++.|. .-.+.+.|..||+.|=..
T Consensus 4 ~C~~C~~~F~--------------~~~rk~~Cr~Cg~~~C~~ 31 (57)
T cd00065 4 SCMGCGKPFT--------------LTRRRHHCRNCGRIFCSK 31 (57)
T ss_pred cCcccCcccc--------------CCccccccCcCcCCcChH
Confidence 4788999993 235778899999998653
No 94
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=58.38 E-value=8.4 Score=37.68 Aligned_cols=71 Identities=23% Similarity=0.422 Sum_probs=46.6
Q ss_pred cCCcccccc--ccccccCcccccccccc-CCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCcccc
Q 041528 373 KRSQFKCLT--CNKVFHSPRSLWGHTAS-HSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNV 449 (527)
Q Consensus 373 ~~~~~~C~~--Cgk~F~~~~~L~~H~~~-H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~ 449 (527)
..++|+|.+ |.+.+.....|..|... |-....-+ -|...+|+. |
T Consensus 346 ~~~~~~~~vp~~~~~~~n~ng~~~~~~~~h~s~i~~~---------------s~~~~ph~~---------~--------- 392 (442)
T KOG4124|consen 346 VDKPYKCPVPNCDKAYKNQNGLKYHKLHGHCSPITTP---------------TPAPIPHQG---------F--------- 392 (442)
T ss_pred ecCCCCCCCCcchhhcccCcceeeccccCcCCCCCCC---------------CCCCCCcce---------e---------
Confidence 468999986 99999999999999755 43322100 001111111 1
Q ss_pred ccccccCCCCCccCCCcCccccchhhhccccc
Q 041528 450 DKRLGSKKSKGHECPFCFRVFKSGQALGGHKR 481 (527)
Q Consensus 450 ~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r 481 (527)
-.-.|+|+|+||.+++.---.|+-|.-
T Consensus 393 -----~~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 393 -----VVENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred -----eeccCcccChhhhhhhccCCCCCceee
Confidence 223699999999999987777777743
No 95
>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=57.33 E-value=3.2 Score=35.20 Aligned_cols=25 Identities=32% Similarity=0.413 Sum_probs=16.4
Q ss_pred CCCccCCCcCccccchhhhccccccccc
Q 041528 458 SKGHECPFCFRVFKSGQALGGHKRSHFV 485 (527)
Q Consensus 458 ekp~~C~iC~k~F~~~~~L~~H~r~H~~ 485 (527)
+.--.|-+|||.|.+ |++|++.|.|
T Consensus 70 ~d~i~clecGk~~k~---LkrHL~~~~g 94 (132)
T PF05443_consen 70 PDYIICLECGKKFKT---LKRHLRTHHG 94 (132)
T ss_dssp SS-EE-TBT--EESB---HHHHHHHTT-
T ss_pred cCeeEEccCCcccch---HHHHHHHccC
Confidence 455779999999976 5999999965
No 96
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=56.62 E-value=5.5 Score=33.34 Aligned_cols=25 Identities=24% Similarity=0.437 Sum_probs=21.9
Q ss_pred eecccCCCccCCchhHHHHhhhhcCCCC
Q 041528 11 FVCKYCNKRYPCGKSLGGHIRTHMNNGN 38 (527)
Q Consensus 11 ~~C~~C~k~f~~~~~L~~H~~~H~~~~p 38 (527)
.+|-.+||.|++ |+||+.+|.+-.|
T Consensus 77 IicLEDGkkfKS---LKRHL~t~~gmTP 101 (148)
T COG4957 77 IICLEDGKKFKS---LKRHLTTHYGLTP 101 (148)
T ss_pred EEEeccCcchHH---HHHHHhcccCCCH
Confidence 469999999985 9999999988766
No 97
>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=56.44 E-value=7.3 Score=31.86 Aligned_cols=15 Identities=33% Similarity=0.868 Sum_probs=12.8
Q ss_pred CccccccccccccCh
Q 041528 97 QEMVCKECGKVFQSL 111 (527)
Q Consensus 97 k~~~C~~Cgk~F~~~ 111 (527)
.|-.|+.||..|.-.
T Consensus 25 ~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 25 DPIVCPKCGTEFPPE 39 (108)
T ss_pred CCccCCCCCCccCcc
Confidence 577899999999876
No 98
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=55.89 E-value=3.5 Score=34.43 Aligned_cols=24 Identities=25% Similarity=0.152 Sum_probs=18.2
Q ss_pred CccCCCcCccccchhhhcccccccccC
Q 041528 460 GHECPFCFRVFKSGQALGGHKRSHFVG 486 (527)
Q Consensus 460 p~~C~iC~k~F~~~~~L~~H~r~H~~~ 486 (527)
-..|-.+||.|. +|++|+.+|.+=
T Consensus 76 ~IicLEDGkkfK---SLKRHL~t~~gm 99 (148)
T COG4957 76 YIICLEDGKKFK---SLKRHLTTHYGL 99 (148)
T ss_pred eEEEeccCcchH---HHHHHHhcccCC
Confidence 355777777775 599999999873
No 99
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.08 E-value=22 Score=29.16 Aligned_cols=22 Identities=14% Similarity=0.225 Sum_probs=17.2
Q ss_pred CCccccccccccccCccccccc
Q 041528 374 RSQFKCLTCNKVFHSPRSLWGH 395 (527)
Q Consensus 374 ~~~~~C~~Cgk~F~~~~~L~~H 395 (527)
+-|.+|.+||-+.-+.-.|.+-
T Consensus 13 ~LP~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 13 ELPVECPICGLTLILSTHLARS 34 (112)
T ss_pred CCCCcCCcCCCEEeccchHHHh
Confidence 3578899999888888777764
No 100
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=54.29 E-value=8.7 Score=24.44 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=17.8
Q ss_pred CCCCCcccccchhhhhccCCCcccccccccccc
Q 041528 77 LRANPKRTRRFVDSNTLTSQQEMVCKECGKVFQ 109 (527)
Q Consensus 77 c~~c~~~~~~~~H~~~h~~~k~~~C~~Cgk~F~ 109 (527)
|+.|...|.+... ++-...+..+|+.||..|.
T Consensus 5 Cp~C~~~y~i~d~-~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 5 CPNCQAKYEIDDE-KIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred CCCCCCEEeCCHH-HCCCCCcEEECCCCCCEeC
Confidence 4444444444332 2334445678999988873
No 101
>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=52.28 E-value=12 Score=23.08 Aligned_cols=26 Identities=19% Similarity=0.227 Sum_probs=16.7
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCcc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRV 469 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~ 469 (527)
|.|..||..+. -....+-+|+.||-.
T Consensus 1 Y~C~~Cg~~~~-------------~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVE-------------LKPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE--------------BSTSSTSSBSSSS-S
T ss_pred CCCCcCCCeeE-------------cCCCCcEECCcCCCe
Confidence 45778888882 122446789999865
No 102
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=51.73 E-value=6.8 Score=29.34 Aligned_cols=21 Identities=24% Similarity=0.528 Sum_probs=17.0
Q ss_pred CCCCCccCC--CcCccccchhhh
Q 041528 456 KKSKGHECP--FCFRVFKSGQAL 476 (527)
Q Consensus 456 t~ekp~~C~--iC~k~F~~~~~L 476 (527)
+.++-+.|. .||.+|.+....
T Consensus 23 ~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 23 TKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred hheeeeecCCCCCCCEEEEEEEE
Confidence 568899998 999999875544
No 103
>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=51.62 E-value=6.2 Score=29.19 Aligned_cols=28 Identities=29% Similarity=0.248 Sum_probs=13.9
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCccccc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKS 472 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~ 472 (527)
..|..|++.|. .-.+.|-|..||..|=.
T Consensus 10 ~~C~~C~~~F~--------------~~~rrhhCr~CG~~vC~ 37 (69)
T PF01363_consen 10 SNCMICGKKFS--------------LFRRRHHCRNCGRVVCS 37 (69)
T ss_dssp SB-TTT--B-B--------------SSS-EEE-TTT--EEEC
T ss_pred CcCcCcCCcCC--------------CceeeEccCCCCCEECC
Confidence 35788999993 22677889999998853
No 104
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=50.75 E-value=8.1 Score=29.80 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=25.7
Q ss_pred CCccccccccccccCccccccccccCCCCCCCCccccccc
Q 041528 374 RSQFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESS 413 (527)
Q Consensus 374 ~~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~ 413 (527)
...|.|..|++. .+.|+-++...|..|++.|+
T Consensus 33 ~~~~~Cp~C~~~--------~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVCPFCGRT--------TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcCCCCCCc--------ceeeeccCeEEcCCCCCeec
Confidence 357999999985 57788888888888888886
No 105
>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=50.56 E-value=9.2 Score=24.44 Aligned_cols=12 Identities=33% Similarity=1.010 Sum_probs=9.4
Q ss_pred cccccccccccc
Q 041528 98 EMVCKECGKVFQ 109 (527)
Q Consensus 98 ~~~C~~Cgk~F~ 109 (527)
...|+.||..|.
T Consensus 25 ~v~C~~C~~~~~ 36 (38)
T TIGR02098 25 KVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEE
Confidence 467999988874
No 106
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=50.45 E-value=12 Score=36.80 Aligned_cols=36 Identities=19% Similarity=0.362 Sum_probs=28.1
Q ss_pred CCCccccccccccccChhhHHHHH-hhhcCCCCCCCc
Q 041528 95 SQQEMVCKECGKVFQSLKALCGHM-ACHSEKDNKMKT 130 (527)
Q Consensus 95 ~~k~~~C~~Cgk~F~~~~~L~~H~-~~H~~~~~~~~~ 130 (527)
....|.|++|++.=-+...|..|. ..|....+..++
T Consensus 76 ~~qSftCPyC~~~Gfte~~f~~Hv~s~Hpda~~~~ic 112 (381)
T KOG1280|consen 76 DPQSFTCPYCGIMGFTERQFGTHVLSQHPEASTSVIC 112 (381)
T ss_pred ccccccCCcccccccchhHHHHHhhhcCcccCcceee
Confidence 345799999999988888999998 788876644443
No 107
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=50.20 E-value=6.6 Score=36.57 Aligned_cols=25 Identities=32% Similarity=0.628 Sum_probs=18.9
Q ss_pred CCceecccCCCccCCchhHHHHhhh
Q 041528 8 KKLFVCKYCNKRYPCGKSLGGHIRT 32 (527)
Q Consensus 8 ~~~~~C~~C~k~f~~~~~L~~H~~~ 32 (527)
++..+|++|++.|.+...+...+++
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 5678899999999987766555543
No 108
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.18 E-value=1.6 Score=39.25 Aligned_cols=29 Identities=21% Similarity=0.253 Sum_probs=22.4
Q ss_pred CCCCccC--CCcCccccchhhhccccc-cccc
Q 041528 457 KSKGHEC--PFCFRVFKSGQALGGHKR-SHFV 485 (527)
Q Consensus 457 ~ekp~~C--~iC~k~F~~~~~L~~H~r-~H~~ 485 (527)
|.--|.| .-|+-.|.+...-+.||- +|.=
T Consensus 141 G~dMy~ClvEgCt~KFkT~r~RkdH~I~~Hk~ 172 (253)
T KOG4173|consen 141 GQDMYQCLVEGCTEKFKTSRDRKDHMIRMHKY 172 (253)
T ss_pred CccHHHHHHHhhhhhhhhhhhhhhHHHHhccC
Confidence 4557888 679999999999999954 5753
No 109
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=49.91 E-value=6.6 Score=36.61 Aligned_cols=25 Identities=32% Similarity=0.611 Sum_probs=21.2
Q ss_pred CCCccCCCcCccccchhhhcccccc
Q 041528 458 SKGHECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 458 ekp~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
+|.+.||+|++.|.++.-+.+..|.
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~ 27 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRV 27 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceE
Confidence 6788999999999998888777664
No 110
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=49.48 E-value=7.7 Score=33.95 Aligned_cols=16 Identities=31% Similarity=0.762 Sum_probs=12.8
Q ss_pred ccccccccccccChhh
Q 041528 98 EMVCKECGKVFQSLKA 113 (527)
Q Consensus 98 ~~~C~~Cgk~F~~~~~ 113 (527)
.|+|+-||++|.+.-.
T Consensus 28 ~~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 28 RRECLACGKRFTTFER 43 (154)
T ss_pred eeeccccCCcceEeEe
Confidence 3889999999987644
No 111
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=48.64 E-value=11 Score=25.27 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=19.2
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCccc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVF 470 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F 470 (527)
|.|..||..|. -...-+.+|+.||-.-
T Consensus 3 Y~C~~Cg~~~~-------------~~~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRENE-------------IKSKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCEee-------------cCCCCceECCCCCceE
Confidence 67888998883 1134678899998654
No 112
>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=47.82 E-value=13 Score=39.58 Aligned_cols=22 Identities=18% Similarity=0.241 Sum_probs=16.5
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCcc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRV 469 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~ 469 (527)
..|.+||... .-|..|+.||..
T Consensus 241 l~Ch~Cg~~~-----------------~~~~~Cp~C~s~ 262 (505)
T TIGR00595 241 LRCHYCGYQE-----------------PIPKTCPQCGSE 262 (505)
T ss_pred EEcCCCcCcC-----------------CCCCCCCCCCCC
Confidence 3466787776 678899999874
No 113
>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=47.48 E-value=4.9 Score=31.41 Aligned_cols=32 Identities=22% Similarity=0.351 Sum_probs=21.5
Q ss_pred CCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccc
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKS 472 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~ 472 (527)
..|.|+.||+.- ..|+-+|. +.|.-|++.|+-
T Consensus 34 ~ky~Cp~Cgk~~----------vkR~a~GI--W~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTS----------VKRVATGI--WKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSE----------EEEEETTE--EEETTTTEEEE-
T ss_pred CCCcCCCCCCce----------eEEeeeEE--eecCCCCCEEeC
Confidence 456788888875 23344444 899999999974
No 114
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=47.17 E-value=13 Score=23.79 Aligned_cols=32 Identities=25% Similarity=0.426 Sum_probs=18.2
Q ss_pred CCCCCcccccchhhhhccCCCcccccccccccc
Q 041528 77 LRANPKRTRRFVDSNTLTSQQEMVCKECGKVFQ 109 (527)
Q Consensus 77 c~~c~~~~~~~~H~~~h~~~k~~~C~~Cgk~F~ 109 (527)
|+.|...|.+... ++..+.+..+|+.|+..|.
T Consensus 5 CP~C~~~f~v~~~-~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 5 CPNCQTRFRVPDD-KLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred CCCCCceEEcCHH-HcccCCcEEECCCCCcEee
Confidence 4444444444322 2334455678999998884
No 115
>PRK12496 hypothetical protein; Provisional
Probab=46.24 E-value=11 Score=33.40 Aligned_cols=27 Identities=15% Similarity=0.037 Sum_probs=16.6
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCcccc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFK 471 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~ 471 (527)
+.|.-||+.|. .....-.|++||..-.
T Consensus 128 ~~C~gC~~~~~--------------~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYP--------------EDYPDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCcccc--------------CCCCCCcCCCCCChhh
Confidence 44778999981 1111134999997643
No 116
>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=46.05 E-value=14 Score=30.26 Aligned_cols=26 Identities=23% Similarity=0.400 Sum_probs=23.4
Q ss_pred cccc----ccccccccChhhHHHHHhhhcC
Q 041528 98 EMVC----KECGKVFQSLKALCGHMACHSE 123 (527)
Q Consensus 98 ~~~C----~~Cgk~F~~~~~L~~H~~~H~~ 123 (527)
-|.| ..|+..+.+...+++|++.++|
T Consensus 80 G~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 80 GYRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred CeeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 3899 9999999999999999987764
No 117
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=45.76 E-value=17 Score=40.33 Aligned_cols=51 Identities=14% Similarity=0.267 Sum_probs=33.7
Q ss_pred CccccccccccccCccccccccccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccccccccc
Q 041528 375 SQFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKRLG 454 (527)
Q Consensus 375 ~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~~~ 454 (527)
....|..||..| .|+.|+.... .+.......|.+||..-
T Consensus 434 ~~l~C~~Cg~v~-----------------~Cp~Cd~~lt----------~H~~~~~L~CH~Cg~~~-------------- 472 (730)
T COG1198 434 PLLLCRDCGYIA-----------------ECPNCDSPLT----------LHKATGQLRCHYCGYQE-------------- 472 (730)
T ss_pred ceeecccCCCcc-----------------cCCCCCcceE----------EecCCCeeEeCCCCCCC--------------
Confidence 355677777654 4777765543 12222455677887664
Q ss_pred cCCCCCccCCCcCcc
Q 041528 455 SKKSKGHECPFCFRV 469 (527)
Q Consensus 455 Ht~ekp~~C~iC~k~ 469 (527)
..|+.|+-||-.
T Consensus 473 ---~~p~~Cp~Cgs~ 484 (730)
T COG1198 473 ---PIPQSCPECGSE 484 (730)
T ss_pred ---CCCCCCCCCCCC
Confidence 799999999976
No 118
>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 KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=43.86 E-value=7.2 Score=36.45 Aligned_cols=49 Identities=14% Similarity=0.200 Sum_probs=38.9
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhcccccccc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKRSHF 484 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~H~ 484 (527)
|.|..||-.- .+..+..|+-.-++ .-|.|--|++.|.. .....|...=+
T Consensus 4 FtCnvCgEsv---KKp~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTCNVCGESV---KKPQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eehhhhhhhc---cccchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 4588888885 55666668877777 88999999999999 88888877643
No 120
>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=43.45 E-value=7.6 Score=34.27 Aligned_cols=31 Identities=13% Similarity=0.009 Sum_probs=19.8
Q ss_pred CCcccccCCCCcccccCccccccccccCCCCCccCCCcCccc
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVF 470 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F 470 (527)
..|.|+.|+.+| +..-.+. --|.|+.||-..
T Consensus 108 ~~Y~Cp~c~~r~--tf~eA~~---------~~F~Cp~Cg~~L 138 (158)
T TIGR00373 108 MFFICPNMCVRF--TFNEAME---------LNFTCPRCGAML 138 (158)
T ss_pred CeEECCCCCcEe--eHHHHHH---------cCCcCCCCCCEe
Confidence 445677777777 3333332 369999999764
No 121
>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=43.39 E-value=11 Score=24.01 Aligned_cols=33 Identities=9% Similarity=-0.096 Sum_probs=18.7
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCccccch
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSG 473 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~ 473 (527)
..|+.||+.| |...-....+=.|++||-.+.++
T Consensus 2 r~C~~Cg~~Y----------h~~~~pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIY----------HIEFNPPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEE----------ETTTB--SSTTBCTTTTEBEBEE
T ss_pred cCcCCCCCcc----------ccccCCCCCCCccCCCCCeeEeC
Confidence 3577787777 11111234457799998766543
No 122
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=43.29 E-value=7.8 Score=34.93 Aligned_cols=32 Identities=16% Similarity=0.128 Sum_probs=20.6
Q ss_pred CCcccccCCCCcccccCccccccccccCCCCCccCCCcCcccc
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFK 471 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~ 471 (527)
..|.|+.|++.| +..-.+ +--|.|+.||-...
T Consensus 116 ~~Y~Cp~C~~ry--tf~eA~---------~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRF--TFDEAM---------EYGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEE--eHHHHh---------hcCCcCCCCCCCCe
Confidence 456677788877 333222 23699999997654
No 123
>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=43.22 E-value=17 Score=30.38 Aligned_cols=20 Identities=25% Similarity=0.285 Sum_probs=15.1
Q ss_pred CCccccccccccccChhhHH
Q 041528 96 QQEMVCKECGKVFQSLKALC 115 (527)
Q Consensus 96 ~k~~~C~~Cgk~F~~~~~L~ 115 (527)
..|-.|+.||..|.-...++
T Consensus 24 k~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 24 RRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred CCCccCCCcCCccCcchhhc
Confidence 35788999999987764544
No 124
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=43.06 E-value=9.5 Score=35.78 Aligned_cols=89 Identities=10% Similarity=-0.035 Sum_probs=52.4
Q ss_pred hhcCCCCcccccccccccccc-----ccccccCCcccccccccCCCccccCCCCCcccccchhhhhc----cCCCccccc
Q 041528 32 THMNNGNSAEAEGEGEVKLNI-----DKIFSGRNIKKDSCFEAGGQSGYVLRANPKRTRRFVDSNTL----TSQQEMVCK 102 (527)
Q Consensus 32 ~H~~~~p~~~C~~C~~~~~~~-----~~~~~~~~~~~~~c~~c~~~~~~~c~~c~~~~~~~~H~~~h----~~~k~~~C~ 102 (527)
+.+|.+.| +|.+|....+-- +........-.|+|..|++.-.|.|-.|. ...---|.+.- ...+++.|+
T Consensus 136 w~hGGrif-~CsfC~~flCEDDQFEHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK-~cfCddHvrrKg~ky~k~k~~PCP 213 (314)
T PF06524_consen 136 WDHGGRIF-KCSFCDNFLCEDDQFEHQASCQVLESETFKCQSCNRLGQYSCLRCK-ICFCDDHVRRKGFKYEKGKPIPCP 213 (314)
T ss_pred ccCCCeEE-EeecCCCeeeccchhhhhhhhhhhhcccccccccccccchhhhhee-eeehhhhhhhcccccccCCCCCCC
Confidence 44566667 777775543222 11111222345777777776666664442 11111244431 234789999
Q ss_pred cccccccChhhHHHHHhhhc
Q 041528 103 ECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 103 ~Cgk~F~~~~~L~~H~~~H~ 122 (527)
-||.-...-..|..-.|.|.
T Consensus 214 KCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 214 KCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCCCcccccccceeeeecch
Confidence 99999988888888888887
No 125
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=42.99 E-value=11 Score=33.88 Aligned_cols=17 Identities=24% Similarity=0.770 Sum_probs=9.0
Q ss_pred CceecccCCCccCCchh
Q 041528 9 KLFVCKYCNKRYPCGKS 25 (527)
Q Consensus 9 ~~~~C~~C~k~f~~~~~ 25 (527)
.-|.|+.|+..|+.-..
T Consensus 116 ~~Y~Cp~C~~rytf~eA 132 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEA 132 (178)
T ss_pred CEEECCCCCcEEeHHHH
Confidence 34556666655554443
No 126
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=42.50 E-value=12 Score=24.31 Aligned_cols=11 Identities=36% Similarity=1.047 Sum_probs=8.4
Q ss_pred ccccccccccc
Q 041528 99 MVCKECGKVFQ 109 (527)
Q Consensus 99 ~~C~~Cgk~F~ 109 (527)
|.|..||..|+
T Consensus 29 y~C~~C~~~wr 39 (39)
T PF01096_consen 29 YVCCNCGHRWR 39 (39)
T ss_dssp EEESSSTEEEE
T ss_pred EEeCCCCCeeC
Confidence 77888887763
No 127
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=41.88 E-value=18 Score=35.43 Aligned_cols=34 Identities=21% Similarity=0.250 Sum_probs=22.4
Q ss_pred ceeccc--CCCccCCchhHHHHhhhhcCCCCcccccccc
Q 041528 10 LFVCKY--CNKRYPCGKSLGGHIRTHMNNGNSAEAEGEG 46 (527)
Q Consensus 10 ~~~C~~--C~k~f~~~~~L~~H~~~H~~~~p~~~C~~C~ 46 (527)
.|.|+. |..+...-..|+.|..+-++. + .|.+|-
T Consensus 151 ~F~CP~skc~~~C~~~k~lk~H~K~~H~~--~-~C~~C~ 186 (493)
T COG5236 151 SFKCPKSKCHRRCGSLKELKKHYKAQHGF--V-LCSECI 186 (493)
T ss_pred HhcCCchhhhhhhhhHHHHHHHHHhhcCc--E-EhHhhh
Confidence 577874 666555567788998864332 3 788883
No 128
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=41.62 E-value=18 Score=24.83 Aligned_cols=24 Identities=17% Similarity=0.325 Sum_probs=17.9
Q ss_pred CCceecccCCCccCCchhHHHHhh
Q 041528 8 KKLFVCKYCNKRYPCGKSLGGHIR 31 (527)
Q Consensus 8 ~~~~~C~~C~k~f~~~~~L~~H~~ 31 (527)
|+.++|..||..|.....=+....
T Consensus 2 Dk~l~C~dCg~~FvfTa~EQ~fy~ 25 (49)
T PF13451_consen 2 DKTLTCKDCGAEFVFTAGEQKFYA 25 (49)
T ss_pred CeeEEcccCCCeEEEehhHHHHHH
Confidence 678889999998888776555443
No 129
>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=41.47 E-value=11 Score=37.55 Aligned_cols=39 Identities=21% Similarity=0.152 Sum_probs=18.4
Q ss_pred CceecccCCCccCCchhHH---HHhh-hhcCCCCccccccccc
Q 041528 9 KLFVCKYCNKRYPCGKSLG---GHIR-THMNNGNSAEAEGEGE 47 (527)
Q Consensus 9 ~~~~C~~C~k~f~~~~~L~---~H~~-~H~~~~p~~~C~~C~~ 47 (527)
+-+.|..|..++-....+- .|.. .|.+.+-||+|..|+.
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~ 293 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGN 293 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCC
Confidence 4578999987766665543 3442 4556666657777743
No 130
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=41.23 E-value=14 Score=34.72 Aligned_cols=41 Identities=20% Similarity=0.391 Sum_probs=30.9
Q ss_pred ccchhhhhccCCCccccccccccccChhhHHHHHhhhcCCCCC
Q 041528 85 RRFVDSNTLTSQQEMVCKECGKVFQSLKALCGHMACHSEKDNK 127 (527)
Q Consensus 85 ~~~~H~~~h~~~k~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~~ 127 (527)
.+..|+-..++ .-|.|--||+.|-. -..+.|..+=++...|
T Consensus 17 ~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCITEaQKY 57 (276)
T KOG2186|consen 17 QVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCITEAQKY 57 (276)
T ss_pred chHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcchHHHh
Confidence 55568877777 67999999999999 6778888765544333
No 131
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=41.04 E-value=13 Score=25.41 Aligned_cols=28 Identities=18% Similarity=0.463 Sum_probs=18.6
Q ss_pred CcccccCCCCcccccCccccccccccCCCCCccCCCcCcc
Q 041528 430 KFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRV 469 (527)
Q Consensus 430 ~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~ 469 (527)
.|.|..||+.|. .-.......|+.||-.
T Consensus 6 ~Y~C~~Cg~~~~------------~~~~~~~irCp~Cg~r 33 (49)
T COG1996 6 EYKCARCGREVE------------LDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEhhhcCCeee------------hhhccCceeCCCCCcE
Confidence 467888888882 1123467889999864
No 132
>PRK04023 DNA polymerase II large subunit; Validated
Probab=41.03 E-value=27 Score=39.63 Aligned_cols=53 Identities=19% Similarity=0.218 Sum_probs=36.1
Q ss_pred CccccccccccccCccccccccccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccccccccc
Q 041528 375 SQFKCLTCNKVFHSPRSLWGHTASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKRLG 454 (527)
Q Consensus 375 ~~~~C~~Cgk~F~~~~~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~~~ 454 (527)
....|..||+.. ....|+.|+..- ...+.|+.||+..
T Consensus 625 g~RfCpsCG~~t--------------~~frCP~CG~~T---------------e~i~fCP~CG~~~-------------- 661 (1121)
T PRK04023 625 GRRKCPSCGKET--------------FYRRCPFCGTHT---------------EPVYRCPRCGIEV-------------- 661 (1121)
T ss_pred cCccCCCCCCcC--------------CcccCCCCCCCC---------------CcceeCccccCcC--------------
Confidence 456788888873 335788777651 2345588998876
Q ss_pred cCCCCCccCCCcCccccchh
Q 041528 455 SKKSKGHECPFCFRVFKSGQ 474 (527)
Q Consensus 455 Ht~ekp~~C~iC~k~F~~~~ 474 (527)
-++.|+-||..-....
T Consensus 662 ----~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 662 ----EEDECEKCGREPTPYS 677 (1121)
T ss_pred ----CCCcCCCCCCCCCccc
Confidence 3578999998765433
No 133
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=40.35 E-value=18 Score=31.20 Aligned_cols=21 Identities=19% Similarity=0.275 Sum_probs=15.3
Q ss_pred CCccCCCcCccccchhhhccc
Q 041528 459 KGHECPFCFRVFKSGQALGGH 479 (527)
Q Consensus 459 kp~~C~iC~k~F~~~~~L~~H 479 (527)
+.=+|..||+.|+|--....-
T Consensus 27 RRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 27 RRRECLECHERFTTFERAELL 47 (147)
T ss_pred ecccCCccCCccceeeecccc
Confidence 456799999999886655443
No 134
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=40.26 E-value=16 Score=32.33 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=11.1
Q ss_pred ccCCCccccccccc
Q 041528 93 LTSQQEMVCKECGK 106 (527)
Q Consensus 93 h~~~k~~~C~~Cgk 106 (527)
|-|+-|-+|++||-
T Consensus 144 ~~ge~P~~CPiCga 157 (166)
T COG1592 144 HEGEAPEVCPICGA 157 (166)
T ss_pred ccCCCCCcCCCCCC
Confidence 45688899999993
No 135
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=39.79 E-value=5.1 Score=43.53 Aligned_cols=22 Identities=18% Similarity=0.389 Sum_probs=15.6
Q ss_pred CCccccccccccccChhhHHHH
Q 041528 96 QQEMVCKECGKVFQSLKALCGH 117 (527)
Q Consensus 96 ~k~~~C~~Cgk~F~~~~~L~~H 117 (527)
-|..+||.|+.+|.-.-.+..|
T Consensus 676 tRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 676 TRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred HhcCCCCCCCCCCCcccccccC
Confidence 3456899999999876554443
No 136
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=39.17 E-value=11 Score=22.43 Aligned_cols=19 Identities=42% Similarity=0.830 Sum_probs=13.1
Q ss_pred cccccccccccCcccccccc
Q 041528 377 FKCLTCNKVFHSPRSLWGHT 396 (527)
Q Consensus 377 ~~C~~Cgk~F~~~~~L~~H~ 396 (527)
|.|-.|++.| .....+.|.
T Consensus 1 ~sCiDC~~~F-~~~~y~~Ht 19 (28)
T PF08790_consen 1 FSCIDCSKDF-DGDSYKSHT 19 (28)
T ss_dssp EEETTTTEEE-EGGGTTT--
T ss_pred CeeecCCCCc-CcCCcCCCC
Confidence 5788999999 556666664
No 137
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=38.61 E-value=21 Score=39.65 Aligned_cols=15 Identities=27% Similarity=0.587 Sum_probs=10.0
Q ss_pred ccCCCcccccccccc
Q 041528 93 LTSQQEMVCKECGKV 107 (527)
Q Consensus 93 h~~~k~~~C~~Cgk~ 107 (527)
|....|..|+.||..
T Consensus 470 ~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 470 YQEPIPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCCCCCC
Confidence 445567778888765
No 138
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=38.54 E-value=7.5 Score=42.07 Aligned_cols=52 Identities=21% Similarity=0.135 Sum_probs=28.6
Q ss_pred CCcCccccchhhhcc--cccccccCCCCCccchhhhhhhhccccCCCCCCCccccc-ccc
Q 041528 464 PFCFRVFKSGQALGG--HKRSHFVGGSEDKTVVIKQELDEMHGLIDLNLPAPVEDE-VIR 520 (527)
Q Consensus 464 ~iC~k~F~~~~~L~~--H~r~H~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 520 (527)
.-+|+-|.--++|.. +.++-.|+++-.=-.++. .....|+++.-+++++ +|.
T Consensus 595 SS~GRlfDAvaalLgi~~~~tYEGE~A~~LEa~a~-----~~~~~~~~~~~~~~~~~vld 649 (750)
T COG0068 595 SSIGRVFDAVAALLGICETRTYEGEAAMALEALAD-----QSDGVDYPYEIKNEDNQVLD 649 (750)
T ss_pred ccccHHHHHHHHHhhhhceeeeccchhhhHHHHhh-----hcccCcccceeccCCccEee
Confidence 457888865555543 556666666633111111 1112777788888876 343
No 139
>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=38.35 E-value=16 Score=32.20 Aligned_cols=19 Identities=16% Similarity=0.548 Sum_probs=11.3
Q ss_pred CCceecccCCCccCCchhH
Q 041528 8 KKLFVCKYCNKRYPCGKSL 26 (527)
Q Consensus 8 ~~~~~C~~C~k~f~~~~~L 26 (527)
..-|.|+.|+..|+.-..+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAM 125 (158)
T ss_pred CCeEECCCCCcEeeHHHHH
Confidence 3446666666666655555
No 140
>PF12907 zf-met2: Zinc-binding
Probab=37.95 E-value=17 Score=23.78 Aligned_cols=29 Identities=24% Similarity=0.476 Sum_probs=20.7
Q ss_pred cccccccccccC---hhhHHHHH-hhhcCCCCC
Q 041528 99 MVCKECGKVFQS---LKALCGHM-ACHSEKDNK 127 (527)
Q Consensus 99 ~~C~~Cgk~F~~---~~~L~~H~-~~H~~~~~~ 127 (527)
++|.+|-.+|.. ...|+.|. ..|++....
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~enKHpK~~~~ 34 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHAENKHPKNTFE 34 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHHHccCCCCCHH
Confidence 679999966654 45699999 578765343
No 141
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=37.46 E-value=22 Score=20.09 Aligned_cols=8 Identities=38% Similarity=0.928 Sum_probs=5.6
Q ss_pred CCCcCccc
Q 041528 463 CPFCFRVF 470 (527)
Q Consensus 463 C~iC~k~F 470 (527)
|+.||..+
T Consensus 16 C~~CG~~l 23 (23)
T PF13240_consen 16 CPNCGTPL 23 (23)
T ss_pred hhhhCCcC
Confidence 88887653
No 142
>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=37.15 E-value=12 Score=30.53 Aligned_cols=25 Identities=24% Similarity=0.448 Sum_probs=22.8
Q ss_pred ccC----CCcCccccchhhhccccccccc
Q 041528 461 HEC----PFCFRVFKSGQALGGHKRSHFV 485 (527)
Q Consensus 461 ~~C----~iC~k~F~~~~~L~~H~r~H~~ 485 (527)
|.| ..|+..+.+..+|..|++.+.|
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 889 9999999999999999987654
No 143
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=36.60 E-value=15 Score=38.90 Aligned_cols=29 Identities=21% Similarity=0.273 Sum_probs=24.0
Q ss_pred CCCCccCCCcCccccchhhhccccccccc
Q 041528 457 KSKGHECPFCFRVFKSGQALGGHKRSHFV 485 (527)
Q Consensus 457 ~ekp~~C~iC~k~F~~~~~L~~H~r~H~~ 485 (527)
..+|..|..||++|........||-+|..
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhh
Confidence 35679999999999988888888777754
No 144
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.60 E-value=8.3 Score=28.79 Aligned_cols=34 Identities=21% Similarity=0.426 Sum_probs=20.5
Q ss_pred cccCCCCCcccccchhhhhccCCCccc-cccccccccCh
Q 041528 74 GYVLRANPKRTRRFVDSNTLTSQQEMV-CKECGKVFQSL 111 (527)
Q Consensus 74 ~~~c~~c~~~~~~~~H~~~h~~~k~~~-C~~Cgk~F~~~ 111 (527)
.|.|..|++.|.+..|++ +-|+. |+.||-.|+..
T Consensus 12 ~Y~c~~cg~~~dvvq~~~----ddplt~ce~c~a~~kk~ 46 (82)
T COG2331 12 SYECTECGNRFDVVQAMT----DDPLTTCEECGARLKKL 46 (82)
T ss_pred EEeecccchHHHHHHhcc----cCccccChhhChHHHHh
Confidence 455666666666554443 44544 99999866544
No 145
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.32 E-value=9.1 Score=33.90 Aligned_cols=18 Identities=22% Similarity=0.490 Sum_probs=12.8
Q ss_pred cCCccccccccccccCcc
Q 041528 373 KRSQFKCLTCNKVFHSPR 390 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~ 390 (527)
++..|.|.+|--.|..+.
T Consensus 128 ~~~~~~CPiCl~~~sek~ 145 (187)
T KOG0320|consen 128 KEGTYKCPICLDSVSEKV 145 (187)
T ss_pred cccccCCCceecchhhcc
Confidence 456688888877776554
No 146
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=35.74 E-value=20 Score=29.57 Aligned_cols=25 Identities=12% Similarity=0.150 Sum_probs=16.4
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCcc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRV 469 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~ 469 (527)
..|..||..|. .....|.||.||..
T Consensus 71 ~~C~~Cg~~~~--------------~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVVE--------------IHQHDAQCPHCHGE 95 (113)
T ss_pred EEcccCCCEEe--------------cCCcCccCcCCCCC
Confidence 34778888872 22355779999843
No 147
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.38 E-value=42 Score=34.38 Aligned_cols=60 Identities=13% Similarity=0.061 Sum_probs=35.1
Q ss_pred cccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhcccccccccCCCCCccchhhhhhhhccccCCC
Q 041528 433 KSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKRSHFVGGSEDKTVVIKQELDEMHGLIDL 508 (527)
Q Consensus 433 c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~H~~~~~~~~~~~~~~~~~~~~~~~~~ 508 (527)
|+.||.+.. -.|..-|+|+-||.++.+.... .--+.-+.+-....++.-.++-...+.+.
T Consensus 353 Cp~Cg~~m~-------------S~G~~g~rC~kCg~~~~~~~~~---~v~r~l~~g~evp~~arRHLskP~~~~~~ 412 (421)
T COG1571 353 CPRCGGRMK-------------SAGRNGFRCKKCGTRARETLIK---EVPRDLEPGVEVPPVARRHLSKPLVLEEA 412 (421)
T ss_pred CCccCCchh-------------hcCCCCcccccccccCCccccc---ccccccCCCCcCCchhhhhccCCcchhhc
Confidence 778999883 3445589999999999876554 11121111114444455555555555444
No 148
>KOG2785 consensus C2H2-type Zn-finger protein [General function prediction only]
Probab=35.05 E-value=6.6 Score=39.05 Aligned_cols=124 Identities=22% Similarity=0.190 Sum_probs=0.0
Q ss_pred cccccccccccCcccccccccc--CC-----CCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCcccc
Q 041528 377 FKCLTCNKVFHSPRSLWGHTAS--HS-----KINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNV 449 (527)
Q Consensus 377 ~~C~~Cgk~F~~~~~L~~H~~~--H~-----~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~ 449 (527)
|.|..|...|.+...-+.|+++ |. ....-| ++=-..|.....+.-.
T Consensus 4 ftC~tC~v~F~~ad~Qr~HyKSdWHRYNLKRkVA~lP---------------------------PItaE~F~~k~~s~~~ 56 (390)
T KOG2785|consen 4 FTCNTCNVEFDDADEQRAHYKSDWHRYNLKRKVASLP---------------------------PITAEEFNEKVLSDDS 56 (390)
T ss_pred ceeeceeeeeccHHHHHHHhhhhHHHhhHHhHhhcCC---------------------------CcCHHHHhHHHhhhhh
Q ss_pred ccccc-cCCCCCccCCCcCccccchhhhcccccc--cccCCCC-----CccchhhhhhhhccccCCCCCC--Cccccccc
Q 041528 450 DKRLG-SKKSKGHECPFCFRVFKSGQALGGHKRS--HFVGGSE-----DKTVVIKQELDEMHGLIDLNLP--APVEDEVI 519 (527)
Q Consensus 450 ~h~~~-Ht~ekp~~C~iC~k~F~~~~~L~~H~r~--H~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~ 519 (527)
.-... -.++-++.|.+|.|.|.+..+...|+.. |....+. ++.+++.++.+-..+-.-.+++ .+..-|+-
T Consensus 57 ~~~~~~e~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~~~r~~e~d~a~~~q~~~~~p~~l~~~~e~e~~~~E~~ 136 (390)
T KOG2785|consen 57 EKEENLEEAESVVYCEACNKSFASPKAHENHLKSKKHVENLSNHQRSEEGDSAKISQLPSRRPSNLQNKGESELKWYEVD 136 (390)
T ss_pred hhhhhhhhcccceehHHhhccccChhhHHHHHHHhhcchhhhhhhccccccchhhhhccccCccccccCCCcccchhhcc
Q ss_pred cc-cCccCC
Q 041528 520 RD-AEFSRW 527 (527)
Q Consensus 520 ~~-~~~~~~ 527 (527)
.| ..-..|
T Consensus 137 ~~~d~~~e~ 145 (390)
T KOG2785|consen 137 SDEDSSEEE 145 (390)
T ss_pred cccccchhh
No 149
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=34.73 E-value=8 Score=37.94 Aligned_cols=76 Identities=16% Similarity=0.101 Sum_probs=30.0
Q ss_pred cccccccccccCccccccccccCCCCC--CCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccccccccc
Q 041528 377 FKCLTCNKVFHSPRSLWGHTASHSKIN--GCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKRLG 454 (527)
Q Consensus 377 ~~C~~Cgk~F~~~~~L~~H~~~H~~~~--~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~~~ 454 (527)
-.|.+||.. +..+.|..--. .|.+ .|..|+..+. ..+..|++||-.-. .. +.....-.
T Consensus 173 g~CPvCGs~-P~~s~l~~~~~--~G~R~L~Cs~C~t~W~--------------~~R~~Cp~Cg~~~~--~~-l~~~~~e~ 232 (290)
T PF04216_consen 173 GYCPVCGSP-PVLSVLRGGER--EGKRYLHCSLCGTEWR--------------FVRIKCPYCGNTDH--EK-LEYFTVEG 232 (290)
T ss_dssp SS-TTT----EEEEEEE--------EEEEEETTT--EEE----------------TTS-TTT---SS---E-EE------
T ss_pred CcCCCCCCc-CceEEEecCCC--CccEEEEcCCCCCeee--------------ecCCCCcCCCCCCC--cc-eeeEecCC
Confidence 358888853 33333333222 2333 7887777775 33566889987752 11 11111223
Q ss_pred cCCCCCccCCCcCccccc
Q 041528 455 SKKSKGHECPFCFRVFKS 472 (527)
Q Consensus 455 Ht~ekp~~C~iC~k~F~~ 472 (527)
-.+.+-+.|..|+-=+++
T Consensus 233 ~~~~rve~C~~C~~YlK~ 250 (290)
T PF04216_consen 233 EPAYRVEVCESCGSYLKT 250 (290)
T ss_dssp --SEEEEEETTTTEEEEE
T ss_pred CCcEEEEECCcccchHHH
Confidence 345677889999865544
No 150
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=34.64 E-value=15 Score=32.01 Aligned_cols=35 Identities=11% Similarity=0.191 Sum_probs=22.8
Q ss_pred cCCccccccccccccCcccccc-ccccCCCCCCCCcccc
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWG-HTASHSKINGCCESIN 410 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~-H~~~H~~~~~C~~c~~ 410 (527)
....|.|..||+.|....++.. ++ ++...|+.|+.
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~---~~~f~Cp~Cg~ 131 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDM---DGTFTCPRCGE 131 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCC---CCcEECCCCCC
Confidence 3467999999999998776654 32 34345554433
No 151
>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=33.95 E-value=22 Score=32.93 Aligned_cols=28 Identities=25% Similarity=0.576 Sum_probs=21.3
Q ss_pred CCCccccccccccccChhhHHHHH-hhhc
Q 041528 95 SQQEMVCKECGKVFQSLKALCGHM-ACHS 122 (527)
Q Consensus 95 ~~k~~~C~~Cgk~F~~~~~L~~H~-~~H~ 122 (527)
++-.|.|.+|+|.|+-.-..+.|+ ..|.
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-H
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCH
Confidence 344599999999999999999999 5566
No 152
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=33.88 E-value=28 Score=22.83 Aligned_cols=24 Identities=21% Similarity=0.418 Sum_probs=16.4
Q ss_pred cccccccccccChh--hHHHHHhhhc
Q 041528 99 MVCKECGKVFQSLK--ALCGHMACHS 122 (527)
Q Consensus 99 ~~C~~Cgk~F~~~~--~L~~H~~~H~ 122 (527)
-.|+.||..|.... .-+.|.+-|.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 47899998887654 4466666664
No 153
>KOG4377 consensus Zn-finger protein [General function prediction only]
Probab=33.79 E-value=60 Score=32.82 Aligned_cols=106 Identities=15% Similarity=0.249 Sum_probs=61.7
Q ss_pred Cceec--ccCCCccCCchhHHHHhhhhcCCCC-----c------ccc--cccccccccc--------ccccccCCccccc
Q 041528 9 KLFVC--KYCNKRYPCGKSLGGHIRTHMNNGN-----S------AEA--EGEGEVKLNI--------DKIFSGRNIKKDS 65 (527)
Q Consensus 9 ~~~~C--~~C~k~f~~~~~L~~H~~~H~~~~p-----~------~~C--~~C~~~~~~~--------~~~~~~~~~~~~~ 65 (527)
.-|.| +.|+..+-.+..+.+|+.+|-..+. | +.| ..|.+...+. .+.+.+...+.|+
T Consensus 270 Ehyhcl~e~C~ykr~~k~DvirH~~~hkkrdnsL~dgf~rfs~syhC~~~~C~ksTsdV~~h~nFht~~~n~Gfrrthfh 349 (480)
T KOG4377|consen 270 EHYHCLNEYCFYKRGQKNDVIRHVEIHKKRDNSLIDGFHRFSNSYHCTGQICEKSTSDVLLHDNFHTDKRNNGFRRTHFH 349 (480)
T ss_pred hhhcccCccccccccchhhhHHHHHHHhhcccccccchhhcCccchhhhcccCcccccccccCccccccccCceecceeE
Confidence 34667 4686666668999999999865332 1 145 5576643333 3344444446778
Q ss_pred ccccCCCccccCCCCCcccccchhhhhc----cC------------CCc------------ccccc--ccccccChhhHH
Q 041528 66 CFEAGGQSGYVLRANPKRTRRFVDSNTL----TS------------QQE------------MVCKE--CGKVFQSLKALC 115 (527)
Q Consensus 66 c~~c~~~~~~~c~~c~~~~~~~~H~~~h----~~------------~k~------------~~C~~--Cgk~F~~~~~L~ 115 (527)
|.-++-.+.+. ...|...| .+ +-+ |-|.. |+.+|...+.+.
T Consensus 350 C~r~gCTdtfK---------~~khk~yh~kdda~~~dGfkkf~k~e~cay~gCkys~~cnhfhc~r~Gc~~tl~s~sqm~ 420 (480)
T KOG4377|consen 350 CQRIGCTDTFK---------DSKHKPYHYKDDAGEIDGFKKFFKDENCAYTGCKYSGICNHFHCDRLGCEATLYSVSQMA 420 (480)
T ss_pred EeccCCccccc---------cccccccccCcchhhhhhhhhhhccccCCccCcccccceeeeeecccCCceEEEehhhhh
Confidence 87776333332 11122111 11 111 22322 899999999999
Q ss_pred HHHhhhcC
Q 041528 116 GHMACHSE 123 (527)
Q Consensus 116 ~H~~~H~~ 123 (527)
.|.|.|..
T Consensus 421 shkrkheR 428 (480)
T KOG4377|consen 421 SHKRKHER 428 (480)
T ss_pred hhhhhhhh
Confidence 99999973
No 154
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=33.63 E-value=30 Score=32.36 Aligned_cols=74 Identities=14% Similarity=0.095 Sum_probs=39.2
Q ss_pred CchhHHHHhhhhcCC-----CCccccccccccccccccccccCCcccccccccCCCccccCCCCCcccccch-hhhhccC
Q 041528 22 CGKSLGGHIRTHMNN-----GNSAEAEGEGEVKLNIDKIFSGRNIKKDSCFEAGGQSGYVLRANPKRTRRFV-DSNTLTS 95 (527)
Q Consensus 22 ~~~~L~~H~~~H~~~-----~p~~~C~~C~~~~~~~~~~~~~~~~~~~~c~~c~~~~~~~c~~c~~~~~~~~-H~~~h~~ 95 (527)
+..+|+.+.+.+.+. +.| .|..|+. .+ ...+-...--..|+.|.++|.-.- .. -.|
T Consensus 91 Te~Nlrm~d~a~~~~ip~~drqF-aC~~Cd~-------~W--------wRrvp~rKeVSRCr~C~~rYDPVP~dk--mwG 152 (278)
T PF15135_consen 91 TEENLRMFDDAQENLIPSVDRQF-ACSSCDH-------MW--------WRRVPQRKEVSRCRKCRKRYDPVPCDK--MWG 152 (278)
T ss_pred hHHHHHHhhhhhhccccccceee-eccccch-------HH--------HhccCcccccccccccccccCCCcccc--ccc
Confidence 445666666665554 445 8888832 11 111111111244555655543221 11 124
Q ss_pred CCccccccccccccChhh
Q 041528 96 QQEMVCKECGKVFQSLKA 113 (527)
Q Consensus 96 ~k~~~C~~Cgk~F~~~~~ 113 (527)
.--|.|+.|+..|+....
T Consensus 153 ~aef~C~~C~h~F~G~~q 170 (278)
T PF15135_consen 153 IAEFHCPKCRHNFRGFAQ 170 (278)
T ss_pred eeeeecccccccchhhhh
Confidence 456999999999997754
No 155
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=33.43 E-value=28 Score=22.71 Aligned_cols=11 Identities=36% Similarity=1.144 Sum_probs=8.6
Q ss_pred ccccccccccc
Q 041528 99 MVCKECGKVFQ 109 (527)
Q Consensus 99 ~~C~~Cgk~F~ 109 (527)
|.|.-||..|+
T Consensus 29 y~C~~C~~~w~ 39 (40)
T smart00440 29 YVCTKCGHRWR 39 (40)
T ss_pred EEeCCCCCEeC
Confidence 78888887765
No 156
>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=33.17 E-value=24 Score=29.23 Aligned_cols=25 Identities=12% Similarity=0.157 Sum_probs=16.3
Q ss_pred ccccCCCCcccccCccccccccccCCCCCccCCCcCccc
Q 041528 432 CKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVF 470 (527)
Q Consensus 432 ~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F 470 (527)
.|..||+.|. ..+..+.||.||...
T Consensus 72 ~C~~Cg~~~~--------------~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 72 ECEDCSEEVS--------------PEIDLYRCPKCHGIM 96 (115)
T ss_pred EcccCCCEEe--------------cCCcCccCcCCcCCC
Confidence 4678888772 223357799998643
No 157
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=33.06 E-value=24 Score=30.71 Aligned_cols=12 Identities=25% Similarity=0.941 Sum_probs=7.8
Q ss_pred cccccccccccc
Q 041528 98 EMVCKECGKVFQ 109 (527)
Q Consensus 98 ~~~C~~Cgk~F~ 109 (527)
.|.|+.||....
T Consensus 123 ~f~Cp~Cg~~l~ 134 (147)
T smart00531 123 TFTCPRCGEELE 134 (147)
T ss_pred cEECCCCCCEEE
Confidence 377777776643
No 158
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=32.93 E-value=32 Score=32.42 Aligned_cols=91 Identities=21% Similarity=0.209 Sum_probs=56.0
Q ss_pred cCCccccccccccccCcccccccccc----CCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCccc
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWGHTAS----HSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTN 448 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~H~~~----H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l 448 (527)
+-+.|.|.+|.. |.....--.|+.+ -...++|..|++-- -|+|-.|.--| ..-..+
T Consensus 139 GGrif~CsfC~~-flCEDDQFEHQAsCQvLe~E~~KC~SCNrlG-----------------q~sCLRCK~cf--CddHvr 198 (314)
T PF06524_consen 139 GGRIFKCSFCDN-FLCEDDQFEHQASCQVLESETFKCQSCNRLG-----------------QYSCLRCKICF--CDDHVR 198 (314)
T ss_pred CCeEEEeecCCC-eeeccchhhhhhhhhhhhccccccccccccc-----------------chhhhheeeee--hhhhhh
Confidence 557888888875 4444444456433 22334676665542 13344454444 333333
Q ss_pred cccccccCCCCCccCCCcCccccchhhhcccccccc
Q 041528 449 VDKRLGSKKSKGHECPFCFRVFKSGQALGGHKRSHF 484 (527)
Q Consensus 449 ~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~H~ 484 (527)
++-.. ..+.+++.||.||..-.....|..=.|+|.
T Consensus 199 rKg~k-y~k~k~~PCPKCg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 199 RKGFK-YEKGKPIPCPKCGYETQETKDLSMSTRSHK 233 (314)
T ss_pred hcccc-cccCCCCCCCCCCCcccccccceeeeecch
Confidence 32222 244589999999999999999999889885
No 159
>PRK05580 primosome assembly protein PriA; Validated
Probab=32.81 E-value=29 Score=38.55 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=8.0
Q ss_pred CCcccccccccc
Q 041528 96 QQEMVCKECGKV 107 (527)
Q Consensus 96 ~k~~~C~~Cgk~ 107 (527)
..|..|+.||..
T Consensus 419 ~~~~~Cp~Cg~~ 430 (679)
T PRK05580 419 PIPKACPECGST 430 (679)
T ss_pred CCCCCCCCCcCC
Confidence 345678888765
No 160
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=32.40 E-value=26 Score=30.18 Aligned_cols=18 Identities=22% Similarity=0.357 Sum_probs=12.6
Q ss_pred CCccCCCcCccccchhhh
Q 041528 459 KGHECPFCFRVFKSGQAL 476 (527)
Q Consensus 459 kp~~C~iC~k~F~~~~~L 476 (527)
+.-.|+.||+.|+|--..
T Consensus 27 RRReC~~C~~RFTTfE~~ 44 (156)
T COG1327 27 RRRECLECGERFTTFERA 44 (156)
T ss_pred hhhcccccccccchhhee
Confidence 456788888888875433
No 161
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=31.64 E-value=29 Score=27.60 Aligned_cols=17 Identities=18% Similarity=0.438 Sum_probs=13.2
Q ss_pred ceecccCCCccCCchhH
Q 041528 10 LFVCKYCNKRYPCGKSL 26 (527)
Q Consensus 10 ~~~C~~C~k~f~~~~~L 26 (527)
||+|.-||..|..-+.+
T Consensus 2 pH~CtrCG~vf~~g~~~ 18 (112)
T COG3364 2 PHQCTRCGEVFDDGSEE 18 (112)
T ss_pred CceecccccccccccHH
Confidence 67888898888886544
No 162
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.63 E-value=32 Score=29.14 Aligned_cols=19 Identities=5% Similarity=-0.129 Sum_probs=10.0
Q ss_pred ccccccCCCCCCCCccccc
Q 041528 393 WGHTASHSKINGCCESINE 411 (527)
Q Consensus 393 ~~H~~~H~~~~~C~~c~~~ 411 (527)
..+++.......||.|...
T Consensus 21 ~~~~~~~~~~~~cP~C~s~ 39 (129)
T COG3677 21 AYAIRMQITKVNCPRCKSS 39 (129)
T ss_pred HHHHhhhcccCcCCCCCcc
Confidence 3455555555566655433
No 163
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=31.05 E-value=16 Score=22.20 Aligned_cols=12 Identities=25% Similarity=0.528 Sum_probs=7.0
Q ss_pred CccCCCcCcccc
Q 041528 460 GHECPFCFRVFK 471 (527)
Q Consensus 460 p~~C~iC~k~F~ 471 (527)
.|.|+-|+..+=
T Consensus 13 kY~Cp~C~~~~C 24 (30)
T PF04438_consen 13 KYRCPRCGARYC 24 (30)
T ss_dssp SEE-TTT--EES
T ss_pred EEECCCcCCcee
Confidence 699999988763
No 164
>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=30.69 E-value=30 Score=36.86 Aligned_cols=11 Identities=27% Similarity=0.760 Sum_probs=6.6
Q ss_pred Ccccccccccc
Q 041528 97 QEMVCKECGKV 107 (527)
Q Consensus 97 k~~~C~~Cgk~ 107 (527)
-|..|+.||..
T Consensus 252 ~~~~Cp~C~s~ 262 (505)
T TIGR00595 252 IPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCCCCC
Confidence 35567777653
No 165
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.28 E-value=25 Score=27.57 Aligned_cols=35 Identities=17% Similarity=0.323 Sum_probs=22.4
Q ss_pred CCCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccchh
Q 041528 428 NSKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQ 474 (527)
Q Consensus 428 ~~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~ 474 (527)
+..|.|+.||+.-. .+. +.-...|.-|++.|+-..
T Consensus 34 ~a~y~CpfCgk~~v----------kR~--a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 34 HAKYFCPFCGKHAV----------KRQ--AVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred hCCccCCCCCCCce----------eee--eeEEEEcCCCCCEEeCCc
Confidence 44677888886641 111 223588999999997543
No 166
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.06 E-value=31 Score=28.72 Aligned_cols=26 Identities=8% Similarity=-0.049 Sum_probs=15.9
Q ss_pred cccccCCCCcccccCccccccccccCCCCCc-cCCCcCccc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGH-ECPFCFRVF 470 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~-~C~iC~k~F 470 (527)
..|..||..|. ..+..| .||.||...
T Consensus 72 ~~C~~Cg~~~~--------------~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 72 LECKDCSHVFK--------------PNALDYGVCEKCHSKN 98 (117)
T ss_pred EEhhhCCCccc--------------cCCccCCcCcCCCCCc
Confidence 34778888882 122234 499998643
No 167
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=29.71 E-value=21 Score=23.63 Aligned_cols=16 Identities=19% Similarity=0.384 Sum_probs=9.9
Q ss_pred CCccCCCcCccccchh
Q 041528 459 KGHECPFCFRVFKSGQ 474 (527)
Q Consensus 459 kp~~C~iC~k~F~~~~ 474 (527)
-||.|+.|++.|=...
T Consensus 12 ~~~~C~~C~~~FC~~H 27 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKH 27 (43)
T ss_dssp SHEE-TTTS-EE-TTT
T ss_pred CCeECCCCCcccCccc
Confidence 5889999999985543
No 168
>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=29.58 E-value=15 Score=25.42 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=15.6
Q ss_pred CceecccCCCccCCchhHHHHhhhhcCCCCccccccc
Q 041528 9 KLFVCKYCNKRYPCGKSLGGHIRTHMNNGNSAEAEGE 45 (527)
Q Consensus 9 ~~~~C~~C~k~f~~~~~L~~H~~~H~~~~p~~~C~~C 45 (527)
..|.|+.|...|-..-.+-.|-..| .|+.|
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~LH-------~CPGC 49 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHETLH-------NCPGC 49 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTTS--------SSSTT
T ss_pred CeEECCCCCCccccCcChhhhcccc-------CCcCC
Confidence 4577888887777666665565555 66666
No 169
>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=29.40 E-value=24 Score=20.27 Aligned_cols=10 Identities=30% Similarity=0.507 Sum_probs=7.8
Q ss_pred CCccCCCcCc
Q 041528 459 KGHECPFCFR 468 (527)
Q Consensus 459 kp~~C~iC~k 468 (527)
-+|.|+-||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4788888884
No 170
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=28.82 E-value=28 Score=37.91 Aligned_cols=18 Identities=22% Similarity=0.372 Sum_probs=12.0
Q ss_pred ccccccccccCccccccc
Q 041528 378 KCLTCNKVFHSPRSLWGH 395 (527)
Q Consensus 378 ~C~~Cgk~F~~~~~L~~H 395 (527)
.|..||-.|+-..+|=.=
T Consensus 125 ~CT~CGPRfTIi~alPYD 142 (750)
T COG0068 125 NCTNCGPRFTIIEALPYD 142 (750)
T ss_pred ccCCCCcceeeeccCCCC
Confidence 477777777776666544
No 171
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.36 E-value=28 Score=29.82 Aligned_cols=12 Identities=25% Similarity=0.373 Sum_probs=8.9
Q ss_pred CCCccCCCcCcc
Q 041528 458 SKGHECPFCFRV 469 (527)
Q Consensus 458 ekp~~C~iC~k~ 469 (527)
..-+.||.||..
T Consensus 105 ~~~~~CP~Cgs~ 116 (135)
T PRK03824 105 HAFLKCPKCGSR 116 (135)
T ss_pred ccCcCCcCCCCC
Confidence 455789999954
No 172
>PF15269 zf-C2H2_7: Zinc-finger
Probab=28.33 E-value=35 Score=22.65 Aligned_cols=21 Identities=24% Similarity=0.404 Sum_probs=14.8
Q ss_pred cccccccccccChhhHHHHHh
Q 041528 99 MVCKECGKVFQSLKALCGHMA 119 (527)
Q Consensus 99 ~~C~~Cgk~F~~~~~L~~H~~ 119 (527)
|+|=.|..+-..++.|-.||+
T Consensus 21 ykcfqcpftc~~kshl~nhmk 41 (54)
T PF15269_consen 21 YKCFQCPFTCNEKSHLFNHMK 41 (54)
T ss_pred ceeecCCcccchHHHHHHHHH
Confidence 556666666677777878876
No 173
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.14 E-value=34 Score=37.77 Aligned_cols=43 Identities=16% Similarity=0.278 Sum_probs=0.0
Q ss_pred cccccccccccCcc---ccccccccCCCCCCCCcccccccCCCcCcCCCCCCCCCCCcccccCCCCcccccCcccccccc
Q 041528 377 FKCLTCNKVFHSPR---SLWGHTASHSKINGCCESINESSENSRETDSFPVPMPNSKFCKSVNGKTPIAQNLSTNVDKRL 453 (527)
Q Consensus 377 ~~C~~Cgk~F~~~~---~L~~H~~~H~~~~~C~~c~~~f~~~~~~~~~~~~~~~~~~~~c~~C~K~f~~~~~~~l~~h~~ 453 (527)
..|..||..+.+.. .|..|. ..+...|..|++.
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~--~~~~l~Ch~CG~~------------------------------------------ 419 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPS--AGGTPRCRWCGRA------------------------------------------ 419 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEec--CCCeeECCCCcCC------------------------------------------
Q ss_pred ccCCCCCccCCCcC
Q 041528 454 GSKKSKGHECPFCF 467 (527)
Q Consensus 454 ~Ht~ekp~~C~iC~ 467 (527)
..|..|+.||
T Consensus 420 ----~~p~~Cp~Cg 429 (665)
T PRK14873 420 ----APDWRCPRCG 429 (665)
T ss_pred ----CcCccCCCCc
No 174
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.89 E-value=37 Score=23.41 Aligned_cols=13 Identities=15% Similarity=0.079 Sum_probs=10.3
Q ss_pred CCccCCCcCcccc
Q 041528 459 KGHECPFCFRVFK 471 (527)
Q Consensus 459 kp~~C~iC~k~F~ 471 (527)
..+.|.-||..+-
T Consensus 36 ~r~~C~~Cgyt~~ 48 (50)
T PRK00432 36 DRWHCGKCGYTEF 48 (50)
T ss_pred CcEECCCcCCEEe
Confidence 5788999998764
No 175
>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=27.24 E-value=25 Score=27.60 Aligned_cols=35 Identities=26% Similarity=0.460 Sum_probs=22.4
Q ss_pred CCCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccchh
Q 041528 428 NSKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQ 474 (527)
Q Consensus 428 ~~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~ 474 (527)
+..|.|+.||+.-. .+.- --...|.-|++.|+-..
T Consensus 33 ~a~y~CpfCgk~~v----------kR~a--~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 33 KAKYVCPFCGKKTV----------KRGS--TGIWTCRKCGAKFAGGA 67 (91)
T ss_pred hcCccCCCCCCCce----------EEEe--eEEEEcCCCCCEEeCCc
Confidence 44677888887641 1111 23588999999997543
No 176
>KOG4124 consensus Putative transcriptional repressor regulating G2/M transition [Transcription; Cell cycle control, cell division, chromosome partitioning]
Probab=27.15 E-value=18 Score=35.49 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=20.8
Q ss_pred cCCCccccccccccccChhhHHHHHh
Q 041528 94 TSQQEMVCKECGKVFQSLKALCGHMA 119 (527)
Q Consensus 94 ~~~k~~~C~~Cgk~F~~~~~L~~H~~ 119 (527)
..-|+|.|+||.++++-...|+-|..
T Consensus 394 ~~nk~~r~~i~~~~~k~~~~l~~~~~ 419 (442)
T KOG4124|consen 394 VENKPYRCEVCSKRYKNLNGLKYHRT 419 (442)
T ss_pred eccCcccChhhhhhhccCCCCCceee
Confidence 45689999999999998877776653
No 177
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=26.84 E-value=35 Score=28.23 Aligned_cols=26 Identities=12% Similarity=0.137 Sum_probs=15.4
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCcc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRV 469 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~ 469 (527)
..|..||..|. ......+.||.||..
T Consensus 71 ~~C~~Cg~~~~-------------~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 71 CWCETCQQYVT-------------LLTQRVRRCPQCHGD 96 (114)
T ss_pred EEcccCCCeee-------------cCCccCCcCcCcCCC
Confidence 34778888772 111112679999954
No 178
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=26.78 E-value=24 Score=33.83 Aligned_cols=34 Identities=21% Similarity=0.238 Sum_probs=23.0
Q ss_pred cccccCCCccccCCCCCcccccchhhhhccCCCccccccccccccCh
Q 041528 65 SCFEAGGQSGYVLRANPKRTRRFVDSNTLTSQQEMVCKECGKVFQSL 111 (527)
Q Consensus 65 ~c~~c~~~~~~~c~~c~~~~~~~~H~~~h~~~k~~~C~~Cgk~F~~~ 111 (527)
.|..||.-|-+.| ...+.++|+ +|++|-..|.-.
T Consensus 253 SaTpCGHiFCWsC------------I~~w~~ek~-eCPlCR~~~~ps 286 (293)
T KOG0317|consen 253 SATPCGHIFCWSC------------ILEWCSEKA-ECPLCREKFQPS 286 (293)
T ss_pred CcCcCcchHHHHH------------HHHHHcccc-CCCcccccCCCc
Confidence 4566777777766 344666666 599998877543
No 179
>PRK12722 transcriptional activator FlhC; Provisional
Probab=26.11 E-value=45 Score=30.15 Aligned_cols=24 Identities=13% Similarity=0.243 Sum_probs=16.6
Q ss_pred cccCCCCcccccCccccccccccCCC--CCccCCCcCc
Q 041528 433 KSVNGKTPIAQNLSTNVDKRLGSKKS--KGHECPFCFR 468 (527)
Q Consensus 433 c~~C~K~f~~~~~~~l~~h~~~Ht~e--kp~~C~iC~k 468 (527)
|..||-.|+ +|..+ ..|.|++|.-
T Consensus 137 C~~Cgg~fv------------~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 137 CNCCGGHFV------------THAHDPVGSFVCGLCQP 162 (187)
T ss_pred CCCCCCCee------------ccccccCCCCcCCCCCC
Confidence 567777774 23333 4899999987
No 180
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=26.09 E-value=18 Score=29.82 Aligned_cols=26 Identities=27% Similarity=0.598 Sum_probs=23.7
Q ss_pred cCCccccccccccccCcccccccccc
Q 041528 373 KRSQFKCLTCNKVFHSPRSLWGHTAS 398 (527)
Q Consensus 373 ~~~~~~C~~Cgk~F~~~~~L~~H~~~ 398 (527)
+-+.|.|-.|.+-|....+|..|.++
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~kt 79 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKT 79 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhc
Confidence 45789999999999999999999876
No 181
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=25.63 E-value=41 Score=35.81 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=25.6
Q ss_pred CCCceecccCCCccCCchhHHHHhhhhcC
Q 041528 7 KKKLFVCKYCNKRYPCGKSLGGHIRTHMN 35 (527)
Q Consensus 7 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~ 35 (527)
.++|.+|..||.+|........||.+|..
T Consensus 415 ~~~pnqC~~CG~R~~~~ee~sk~md~H~d 443 (579)
T KOG2071|consen 415 KDSPNQCKSCGLRFDDSEERSKHMDIHDD 443 (579)
T ss_pred cCCcchhcccccccccchhhhhHhhhhhh
Confidence 36789999999999999999999988864
No 182
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=25.23 E-value=20 Score=36.70 Aligned_cols=23 Identities=26% Similarity=0.374 Sum_probs=21.1
Q ss_pred CccCCCcCccccchhhhcccccc
Q 041528 460 GHECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 460 p~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
...|.-|+..|.++..|-.|++.
T Consensus 460 ~~~C~tCr~~FdSRnkLF~Hlk~ 482 (508)
T KOG0717|consen 460 LISCTTCRESFDSRNKLFAHLKK 482 (508)
T ss_pred hHhhhhhhhhccchhHHHHHhhh
Confidence 37899999999999999999876
No 183
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=24.75 E-value=42 Score=36.73 Aligned_cols=14 Identities=29% Similarity=0.607 Sum_probs=11.5
Q ss_pred cccccccccccCcc
Q 041528 377 FKCLTCNKVFHSPR 390 (527)
Q Consensus 377 ~~C~~Cgk~F~~~~ 390 (527)
-.|..|++.|....
T Consensus 461 dtC~~C~kkFfSls 474 (1374)
T PTZ00303 461 DSCPSCGRAFISLS 474 (1374)
T ss_pred CcccCcCCcccccc
Confidence 56999999998763
No 184
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=24.45 E-value=27 Score=24.35 Aligned_cols=12 Identities=33% Similarity=0.811 Sum_probs=6.5
Q ss_pred cCCCcCccccch
Q 041528 462 ECPFCFRVFKSG 473 (527)
Q Consensus 462 ~C~iC~k~F~~~ 473 (527)
.||+|++.|..-
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 799999999743
No 185
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=24.41 E-value=46 Score=23.35 Aligned_cols=29 Identities=21% Similarity=0.189 Sum_probs=20.8
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCccccch
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSG 473 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~ 473 (527)
-.|..||+.|. .++---.|+.||..+-+.
T Consensus 6 ~~C~~Cg~~~~--------------~~dDiVvCp~CgapyHR~ 34 (54)
T PF14446_consen 6 CKCPVCGKKFK--------------DGDDIVVCPECGAPYHRD 34 (54)
T ss_pred ccChhhCCccc--------------CCCCEEECCCCCCcccHH
Confidence 35888999982 356677899998876543
No 186
>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=24.40 E-value=47 Score=21.92 Aligned_cols=19 Identities=16% Similarity=0.029 Sum_probs=10.2
Q ss_pred ccccCCCCCCCCccccccc
Q 041528 395 HTASHSKINGCCESINESS 413 (527)
Q Consensus 395 H~~~H~~~~~C~~c~~~f~ 413 (527)
|.+.+...+.|+.|++.|+
T Consensus 1 ~kK~~lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 1 HKKSNLPSKICPVCGRPFT 19 (42)
T ss_pred CCcccCCCCcCcccCCcch
Confidence 3444555556665555554
No 187
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=24.13 E-value=1.1e+02 Score=30.04 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=17.1
Q ss_pred ccccccccccccChhhHHHHHhhhc
Q 041528 98 EMVCKECGKVFQSLKALCGHMACHS 122 (527)
Q Consensus 98 ~~~C~~Cgk~F~~~~~L~~H~~~H~ 122 (527)
.|.|+.|...|.-.-+.-.|-..|-
T Consensus 345 ~y~C~~Ck~~FCldCDv~iHesLh~ 369 (378)
T KOG2807|consen 345 RYRCESCKNVFCLDCDVFIHESLHN 369 (378)
T ss_pred cEEchhccceeeccchHHHHhhhhc
Confidence 4777777777777776666665553
No 188
>KOG2636 consensus Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=24.09 E-value=48 Score=33.90 Aligned_cols=29 Identities=28% Similarity=0.455 Sum_probs=24.9
Q ss_pred hhccCCCcccccccc-ccccChhhHHHHHh
Q 041528 91 NTLTSQQEMVCKECG-KVFQSLKALCGHMA 119 (527)
Q Consensus 91 ~~h~~~k~~~C~~Cg-k~F~~~~~L~~H~~ 119 (527)
+.|--.+.|.|+||| .+|..+..+.+|..
T Consensus 394 KLHGL~~ey~CEICGNy~Y~GrkaF~RHF~ 423 (497)
T KOG2636|consen 394 KLHGLDIEYNCEICGNYVYKGRKAFDRHFN 423 (497)
T ss_pred hhcCCCcccceeeccCccccCcHHHHHHhH
Confidence 456667789999999 89999999999984
No 189
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.75 E-value=80 Score=34.74 Aligned_cols=12 Identities=25% Similarity=0.387 Sum_probs=7.8
Q ss_pred cCCCcCccccch
Q 041528 462 ECPFCFRVFKSG 473 (527)
Q Consensus 462 ~C~iC~k~F~~~ 473 (527)
-|+.||....+.
T Consensus 43 fC~~CG~~~~~~ 54 (645)
T PRK14559 43 HCPNCGAETGTI 54 (645)
T ss_pred cccccCCcccch
Confidence 477777776543
No 190
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=23.75 E-value=48 Score=23.35 Aligned_cols=17 Identities=29% Similarity=0.655 Sum_probs=13.8
Q ss_pred CCCCCccCCCcCccccc
Q 041528 456 KKSKGHECPFCFRVFKS 472 (527)
Q Consensus 456 t~ekp~~C~iC~k~F~~ 472 (527)
.+++---|++|++.|..
T Consensus 35 ~~~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 35 PGERYNGCPFCGTPFEF 51 (55)
T ss_pred ChhhccCCCCCCCcccC
Confidence 46777889999999865
No 191
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=23.62 E-value=37 Score=27.12 Aligned_cols=20 Identities=40% Similarity=0.506 Sum_probs=16.1
Q ss_pred cccccCCCCCccCCCcCcccc
Q 041528 451 KRLGSKKSKGHECPFCFRVFK 471 (527)
Q Consensus 451 h~~~Ht~ekp~~C~iC~k~F~ 471 (527)
-+..+.| +|++|+.||.-|.
T Consensus 71 W~~l~~g-~~~rC~eCG~~fk 90 (97)
T cd00924 71 WMWLEKG-KPKRCPECGHVFK 90 (97)
T ss_pred EEEEeCC-CceeCCCCCcEEE
Confidence 3556666 8999999999886
No 192
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=23.54 E-value=31 Score=27.03 Aligned_cols=34 Identities=24% Similarity=0.362 Sum_probs=21.7
Q ss_pred CCCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccch
Q 041528 428 NSKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSG 473 (527)
Q Consensus 428 ~~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~ 473 (527)
+..|.|+.||+.-. .|.- --...|.-|++.|+-.
T Consensus 34 ~a~y~CpfCgk~~v----------kR~a--~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 34 RAKHVCPVCGRPKV----------KRVG--TGIWECRKCGAKFAGG 67 (90)
T ss_pred hcCccCCCCCCCce----------EEEE--EEEEEcCCCCCEEeCC
Confidence 44677888876641 1111 2358899999999753
No 193
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=23.51 E-value=56 Score=22.29 Aligned_cols=25 Identities=20% Similarity=0.049 Sum_probs=16.1
Q ss_pred CccCCCcCccccchhh-hcccccccc
Q 041528 460 GHECPFCFRVFKSGQA-LGGHKRSHF 484 (527)
Q Consensus 460 p~~C~iC~k~F~~~~~-L~~H~r~H~ 484 (527)
.|.|+.||..|.-... +..+...+.
T Consensus 20 ~~vC~~Cg~~~~~~~~~~~~~~~~~~ 45 (52)
T smart00661 20 RFVCRKCGYEEPIEQKYVYKEKLKHS 45 (52)
T ss_pred EEECCcCCCeEECCCcEEEEEEeccc
Confidence 6889999988876544 333433333
No 194
>PHA02998 RNA polymerase subunit; Provisional
Probab=23.43 E-value=45 Score=29.59 Aligned_cols=39 Identities=15% Similarity=0.253 Sum_probs=22.4
Q ss_pred cccCCCCCcccccchhhhhccCCCc----cccccccccccChh
Q 041528 74 GYVLRANPKRTRRFVDSNTLTSQQE----MVCKECGKVFQSLK 112 (527)
Q Consensus 74 ~~~c~~c~~~~~~~~H~~~h~~~k~----~~C~~Cgk~F~~~~ 112 (527)
...|+.|+..-.....+++-.+..| |.|..||+.|+-+.
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCcc
Confidence 3455555533333333344444434 89999999987553
No 195
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=23.39 E-value=54 Score=36.01 Aligned_cols=17 Identities=12% Similarity=0.122 Sum_probs=11.9
Q ss_pred ccccccccCCCccccCC
Q 041528 62 KKDSCFEAGGQSGYVLR 78 (527)
Q Consensus 62 ~~~~c~~c~~~~~~~c~ 78 (527)
+.|+|+.||..|-..|.
T Consensus 480 RKHHCRkCGrVFC~~CS 496 (1374)
T PTZ00303 480 RAHHCRSCGIRLCVFCI 496 (1374)
T ss_pred ccccccCCccccCcccc
Confidence 45688888887755553
No 196
>PRK01343 zinc-binding protein; Provisional
Probab=23.35 E-value=51 Score=23.44 Aligned_cols=11 Identities=27% Similarity=0.600 Sum_probs=5.9
Q ss_pred ccCCCcCcccc
Q 041528 461 HECPFCFRVFK 471 (527)
Q Consensus 461 ~~C~iC~k~F~ 471 (527)
..|++|+|.|.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 44555555553
No 197
>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=23.28 E-value=52 Score=24.13 Aligned_cols=32 Identities=13% Similarity=0.194 Sum_probs=22.4
Q ss_pred CCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccc
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKS 472 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~ 472 (527)
++-.|+.||..-. . -...+-|.|+.||..+..
T Consensus 27 TSq~C~~CG~~~~--~----------~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 27 TSQTCPRCGHRNK--K----------RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccCcccccc--c----------ccccceEEcCCCCCEECc
Confidence 4556888888772 1 234678999999988653
No 198
>COG1773 Rubredoxin [Energy production and conversion]
Probab=23.18 E-value=34 Score=24.12 Aligned_cols=14 Identities=29% Similarity=0.717 Sum_probs=10.4
Q ss_pred ccccccccccccCh
Q 041528 98 EMVCKECGKVFQSL 111 (527)
Q Consensus 98 ~~~C~~Cgk~F~~~ 111 (527)
.|+|.+||..|.-.
T Consensus 3 ~~~C~~CG~vYd~e 16 (55)
T COG1773 3 RWRCSVCGYVYDPE 16 (55)
T ss_pred ceEecCCceEeccc
Confidence 57888888888654
No 199
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.89 E-value=41 Score=34.60 Aligned_cols=24 Identities=29% Similarity=0.652 Sum_probs=21.2
Q ss_pred CccccccccccccCcccccccccc
Q 041528 375 SQFKCLTCNKVFHSPRSLWGHTAS 398 (527)
Q Consensus 375 ~~~~C~~Cgk~F~~~~~L~~H~~~ 398 (527)
-...|..|+..|.++..|-.|+..
T Consensus 459 a~~~C~tCr~~FdSRnkLF~Hlk~ 482 (508)
T KOG0717|consen 459 ALISCTTCRESFDSRNKLFAHLKK 482 (508)
T ss_pred hhHhhhhhhhhccchhHHHHHhhh
Confidence 347899999999999999999765
No 200
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.78 E-value=46 Score=22.71 Aligned_cols=27 Identities=26% Similarity=0.673 Sum_probs=17.4
Q ss_pred CCCccCCCc------Cccccchhhhcccccccc
Q 041528 458 SKGHECPFC------FRVFKSGQALGGHKRSHF 484 (527)
Q Consensus 458 ekp~~C~iC------~k~F~~~~~L~~H~r~H~ 484 (527)
...|+|..| ..-|.....-..|...|.
T Consensus 13 g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~ 45 (49)
T cd02335 13 TIRIKCAECPDFDLCLECFSAGAEIGKHRNDHN 45 (49)
T ss_pred CcEEECCCCCCcchhHHhhhCcCCCCCCCCCCC
Confidence 355666555 556677666677777774
No 201
>PRK05580 primosome assembly protein PriA; Validated
Probab=22.66 E-value=58 Score=36.22 Aligned_cols=22 Identities=18% Similarity=0.238 Sum_probs=16.6
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCcc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRV 469 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~ 469 (527)
..|.+||... ..|..|+.||..
T Consensus 409 l~Ch~Cg~~~-----------------~~~~~Cp~Cg~~ 430 (679)
T PRK05580 409 LRCHHCGYQE-----------------PIPKACPECGST 430 (679)
T ss_pred EECCCCcCCC-----------------CCCCCCCCCcCC
Confidence 3466787776 678889999776
No 202
>PF12773 DZR: Double zinc ribbon
Probab=22.33 E-value=1.3e+02 Score=20.23 Aligned_cols=8 Identities=38% Similarity=0.816 Sum_probs=3.4
Q ss_pred ccCCCcCc
Q 041528 461 HECPFCFR 468 (527)
Q Consensus 461 ~~C~iC~k 468 (527)
..|+.||.
T Consensus 30 ~~C~~Cg~ 37 (50)
T PF12773_consen 30 KICPNCGA 37 (50)
T ss_pred CCCcCCcC
Confidence 33444444
No 203
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=22.29 E-value=19 Score=39.29 Aligned_cols=33 Identities=18% Similarity=0.280 Sum_probs=25.4
Q ss_pred cccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhcccc
Q 041528 433 KSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHK 480 (527)
Q Consensus 433 c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~ 480 (527)
|..|-+++. .-|.=+||.|+.+|+...-+..|+
T Consensus 666 C~~Cvq~r~---------------etRqRKCP~Cn~aFganDv~~I~l 698 (698)
T KOG0978|consen 666 CEECVQTRY---------------ETRQRKCPKCNAAFGANDVHRIHL 698 (698)
T ss_pred HHHHHHHHH---------------HHhcCCCCCCCCCCCcccccccCC
Confidence 777777772 456678999999999888777664
No 204
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=22.27 E-value=49 Score=28.20 Aligned_cols=36 Identities=19% Similarity=0.198 Sum_probs=29.1
Q ss_pred CCCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhcccccc
Q 041528 428 NSKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKRS 482 (527)
Q Consensus 428 ~~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r~ 482 (527)
..+..|.+|| | .-+|.|--||-.+=+..-|+.|..|
T Consensus 116 P~r~fCaVCG--~-----------------~S~ysC~~CG~kyCsv~C~~~HneT 151 (156)
T KOG3362|consen 116 PLRKFCAVCG--Y-----------------DSKYSCVNCGTKYCSVRCLKTHNET 151 (156)
T ss_pred CcchhhhhcC--C-----------------CchhHHHhcCCceeechhhhhcccc
Confidence 4455699999 5 4679999999999999999988643
No 205
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=22.26 E-value=62 Score=19.45 Aligned_cols=8 Identities=25% Similarity=0.488 Sum_probs=6.6
Q ss_pred CccCCCcC
Q 041528 460 GHECPFCF 467 (527)
Q Consensus 460 p~~C~iC~ 467 (527)
-|.|..|+
T Consensus 15 ~Y~C~~c~ 22 (30)
T PF03107_consen 15 FYHCSECC 22 (30)
T ss_pred eEEeCCCC
Confidence 68888887
No 206
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=22.16 E-value=69 Score=22.60 Aligned_cols=15 Identities=27% Similarity=0.372 Sum_probs=11.3
Q ss_pred CCCCccCCCcCcccc
Q 041528 457 KSKGHECPFCFRVFK 471 (527)
Q Consensus 457 ~ekp~~C~iC~k~F~ 471 (527)
+.-.|.|+.||-.+-
T Consensus 11 ~~v~~~Cp~cGipth 25 (55)
T PF13824_consen 11 AHVNFECPDCGIPTH 25 (55)
T ss_pred cccCCcCCCCCCcCc
Confidence 456799999997763
No 207
>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=22.03 E-value=21 Score=29.41 Aligned_cols=26 Identities=15% Similarity=0.016 Sum_probs=15.0
Q ss_pred cccccCCCCcccccCccccccccccCCCCCccCCCcCccc
Q 041528 431 FCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVF 470 (527)
Q Consensus 431 ~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F 470 (527)
..|..||+.|. .....+.||.||...
T Consensus 71 ~~C~~Cg~~~~--------------~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 71 ARCRDCGHEFE--------------PDEFDFSCPRCGSPD 96 (113)
T ss_dssp EEETTTS-EEE--------------CHHCCHH-SSSSSS-
T ss_pred EECCCCCCEEe--------------cCCCCCCCcCCcCCC
Confidence 34778888883 122337799998763
No 208
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=21.96 E-value=26 Score=31.46 Aligned_cols=14 Identities=36% Similarity=0.873 Sum_probs=7.6
Q ss_pred CceecccCCCccCC
Q 041528 9 KLFVCKYCNKRYPC 22 (527)
Q Consensus 9 ~~~~C~~C~k~f~~ 22 (527)
.||.|.+|.+.|..
T Consensus 195 IPF~C~iCKkdy~s 208 (259)
T COG5152 195 IPFLCGICKKDYES 208 (259)
T ss_pred Cceeehhchhhccc
Confidence 45555555555543
No 209
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=21.91 E-value=57 Score=25.72 Aligned_cols=40 Identities=10% Similarity=-0.007 Sum_probs=16.5
Q ss_pred CCCceecccCCCccCCchhHHHHhhhhcCCCCcccccccccccccc
Q 041528 7 KKKLFVCKYCNKRYPCGKSLGGHIRTHMNNGNSAEAEGEGEVKLNI 52 (527)
Q Consensus 7 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~~p~~~C~~C~~~~~~~ 52 (527)
+.+.-.|.+||+.+.-.. ..-.|++.||-|+.|-+.|.++
T Consensus 11 g~ke~~CalCG~tWg~~y------~Ev~G~rLfFCCd~ca~EF~nm 50 (105)
T PF11494_consen 11 GTKEMGCALCGATWGDYY------EEVDGERLFFCCDDCAKEFKNM 50 (105)
T ss_dssp -SGGGS-SS---S---SS-------B-TT--BSSS--SSSS-TTS-
T ss_pred ccccccccccCCcHHHHH------HhhcCCEEEEEcHHHHHHHHHH
Confidence 345677999999887432 3456788886778887666555
No 210
>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=21.81 E-value=31 Score=21.68 Aligned_cols=15 Identities=27% Similarity=0.509 Sum_probs=6.2
Q ss_pred cCCCcCccccchhhh
Q 041528 462 ECPFCFRVFKSGQAL 476 (527)
Q Consensus 462 ~C~iC~k~F~~~~~L 476 (527)
.|..|++.|..+.-+
T Consensus 5 ~C~eC~~~f~dSyL~ 19 (34)
T PF01286_consen 5 KCDECGKPFMDSYLL 19 (34)
T ss_dssp E-TTT--EES-SSCC
T ss_pred hHhHhCCHHHHHHHH
Confidence 466677766654433
No 211
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=21.60 E-value=29 Score=34.09 Aligned_cols=26 Identities=27% Similarity=0.655 Sum_probs=23.1
Q ss_pred CCccCCCcCccccchhhhcccccc--cc
Q 041528 459 KGHECPFCFRVFKSGQALGGHKRS--HF 484 (527)
Q Consensus 459 kp~~C~iC~k~F~~~~~L~~H~r~--H~ 484 (527)
-.+.|-.|.|.|..+-.|+.|||. |.
T Consensus 194 ~r~~CLyCekifrdkntLkeHMrkK~Hr 221 (423)
T KOG2482|consen 194 ERLRCLYCEKIFRDKNTLKEHMRKKRHR 221 (423)
T ss_pred hhheeeeeccccCCcHHHHHHHHhccCc
Confidence 368999999999999999999985 54
No 212
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=21.48 E-value=56 Score=31.71 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=27.7
Q ss_pred CCcccccCCCCcccccCccccccccccCCCCCccCCCcCccccchhhhccccc
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRVFKSGQALGGHKR 481 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~F~~~~~L~~H~r 481 (527)
....|.+||+.| +.|+|+-|+-.+=+-.-.+.|.-
T Consensus 6 ~~~~C~ic~vq~------------------~~YtCPRCn~~YCsl~CYr~h~~ 40 (383)
T KOG4317|consen 6 SFLACGICGVQK------------------REYTCPRCNLLYCSLKCYRNHKH 40 (383)
T ss_pred ceeecccccccc------------------ccccCCCCCccceeeeeecCCCc
Confidence 345689999998 34999999999988777777754
No 213
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=21.25 E-value=46 Score=28.09 Aligned_cols=12 Identities=50% Similarity=1.027 Sum_probs=5.9
Q ss_pred CccCCCcCcccc
Q 041528 460 GHECPFCFRVFK 471 (527)
Q Consensus 460 p~~C~iC~k~F~ 471 (527)
||+|.-||+.|.
T Consensus 1 PH~Ct~Cg~~f~ 12 (131)
T PF09845_consen 1 PHQCTKCGRVFE 12 (131)
T ss_pred CcccCcCCCCcC
Confidence 344555555554
No 214
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.06 E-value=54 Score=27.80 Aligned_cols=16 Identities=38% Similarity=0.806 Sum_probs=10.9
Q ss_pred CCccccccccccccCh
Q 041528 96 QQEMVCKECGKVFQSL 111 (527)
Q Consensus 96 ~k~~~C~~Cgk~F~~~ 111 (527)
...|.|..|++.|.-.
T Consensus 51 ~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 51 HQRYKCKSCGSTFTVE 66 (129)
T ss_pred ccccccCCcCcceeee
Confidence 4457777777777654
No 215
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=20.93 E-value=51 Score=32.45 Aligned_cols=29 Identities=28% Similarity=0.542 Sum_probs=23.8
Q ss_pred ceecccCCCccCCchhHHHHhhh--hcCCCC
Q 041528 10 LFVCKYCNKRYPCGKSLGGHIRT--HMNNGN 38 (527)
Q Consensus 10 ~~~C~~C~k~f~~~~~L~~H~~~--H~~~~p 38 (527)
.+.|-.|.|.|+.+..|+.|||. |...-|
T Consensus 195 r~~CLyCekifrdkntLkeHMrkK~HrrinP 225 (423)
T KOG2482|consen 195 RLRCLYCEKIFRDKNTLKEHMRKKRHRRINP 225 (423)
T ss_pred hheeeeeccccCCcHHHHHHHHhccCcccCC
Confidence 47899999999999999999984 544333
No 216
>PRK05978 hypothetical protein; Provisional
Probab=20.64 E-value=66 Score=27.96 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=5.6
Q ss_pred cccccccccCh
Q 041528 101 CKECGKVFQSL 111 (527)
Q Consensus 101 C~~Cgk~F~~~ 111 (527)
|++||..|...
T Consensus 55 C~~CG~~~~~~ 65 (148)
T PRK05978 55 CAACGEDFTHH 65 (148)
T ss_pred ccccCCccccC
Confidence 55555555444
No 217
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.64 E-value=35 Score=34.82 Aligned_cols=36 Identities=11% Similarity=0.061 Sum_probs=20.2
Q ss_pred CCcccccCCCCcccccCccccccccccCCCCCccCCCcCcc
Q 041528 429 SKFCKSVNGKTPIAQNLSTNVDKRLGSKKSKGHECPFCFRV 469 (527)
Q Consensus 429 ~~~~c~~C~K~f~~~~~~~l~~h~~~Ht~ekp~~C~iC~k~ 469 (527)
..|.|+.|.++| .. |..-++.-.-.-.|.|..|+=-
T Consensus 127 ~~Y~Cp~C~kky--t~---Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 127 AGYVCPNCQKKY--TS---LEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccCCccccch--hh---hHHHHhhcccCceEEEecCCCc
Confidence 445566777777 33 3333333333456888888743
No 218
>PRK12860 transcriptional activator FlhC; Provisional
Probab=20.60 E-value=67 Score=29.11 Aligned_cols=23 Identities=13% Similarity=0.257 Sum_probs=15.9
Q ss_pred cccCCCCcccccCccccccccccCCC--CCccCCCcC
Q 041528 433 KSVNGKTPIAQNLSTNVDKRLGSKKS--KGHECPFCF 467 (527)
Q Consensus 433 c~~C~K~f~~~~~~~l~~h~~~Ht~e--kp~~C~iC~ 467 (527)
|..||-.|+ +|..+ ..|.|++|.
T Consensus 137 C~~Cgg~fv------------~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 137 CCRCGGKFV------------THAHDLRHNFVCGLCQ 161 (189)
T ss_pred CCCCCCCee------------ccccccCCCCcCCCCC
Confidence 567777773 23333 489999998
No 219
>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=20.38 E-value=42 Score=31.15 Aligned_cols=30 Identities=17% Similarity=0.347 Sum_probs=22.3
Q ss_pred CCCceecccCCCccCCchhHHHHhhhhcCC
Q 041528 7 KKKLFVCKYCNKRYPCGKSLGGHIRTHMNN 36 (527)
Q Consensus 7 ~~~~~~C~~C~k~f~~~~~L~~H~~~H~~~ 36 (527)
++..|.|..|+|.|+-..=.+.||..-+.+
T Consensus 74 ~~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 74 DEDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SSEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred cCCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 456799999999999999999999864433
No 220
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=20.22 E-value=48 Score=28.68 Aligned_cols=35 Identities=14% Similarity=0.242 Sum_probs=22.0
Q ss_pred CCccccCCCCCcccccch-hhhhccCCCcccccccccc
Q 041528 71 GQSGYVLRANPKRTRRFV-DSNTLTSQQEMVCKECGKV 107 (527)
Q Consensus 71 ~~~~~~c~~c~~~~~~~~-H~~~h~~~k~~~C~~Cgk~ 107 (527)
+.|.|.|. |+..+...+ |-.+-.|+ .|.|..|+-.
T Consensus 114 ~~~~Y~C~-C~q~~l~~RRhn~~~~g~-~YrC~~C~gk 149 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRIRRHNTVRRGE-VYRCGKCGGK 149 (156)
T ss_pred cceeEEee-cCCccchhhhcccccccc-eEEeccCCce
Confidence 56677776 765543332 44444566 7999998754
Done!