Query psy4404
Match_columns 151
No_of_seqs 123 out of 2185
Neff 10.3
Searched_HMMs 46136
Date Sat Aug 17 00:41:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4404hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2462|consensus 99.9 6.4E-27 1.4E-31 160.0 6.2 121 3-131 130-250 (279)
2 KOG2462|consensus 99.9 6E-26 1.3E-30 155.3 4.7 107 2-119 160-266 (279)
3 KOG3576|consensus 99.7 4.5E-18 9.7E-23 112.1 2.4 116 2-126 116-242 (267)
4 KOG1074|consensus 99.7 3.2E-18 7E-23 131.9 1.1 53 69-121 606-658 (958)
5 KOG3608|consensus 99.6 2.4E-16 5.2E-21 111.7 4.4 117 1-127 205-322 (467)
6 KOG3623|consensus 99.6 1.5E-16 3.2E-21 121.5 0.6 109 2-118 209-331 (1007)
7 KOG3623|consensus 99.6 3.8E-16 8.3E-21 119.2 1.2 83 34-118 890-972 (1007)
8 KOG1074|consensus 99.6 2E-15 4.4E-20 116.7 3.7 59 69-127 880-938 (958)
9 KOG3576|consensus 99.5 2.2E-15 4.7E-20 99.6 1.5 85 35-121 114-198 (267)
10 KOG3608|consensus 99.4 4.8E-13 1E-17 95.1 5.4 109 4-121 264-377 (467)
11 PHA00733 hypothetical protein 99.2 3.8E-11 8.2E-16 75.8 4.7 87 31-121 33-124 (128)
12 PLN03086 PRLI-interacting fact 99.2 1E-10 2.2E-15 89.3 7.7 58 44-106 457-514 (567)
13 PLN03086 PRLI-interacting fact 99.1 3E-10 6.4E-15 86.9 7.0 102 3-120 453-564 (567)
14 PHA00733 hypothetical protein 99.0 3.3E-10 7.1E-15 71.6 3.8 86 2-93 39-124 (128)
15 PHA02768 hypothetical protein; 98.9 7.8E-10 1.7E-14 58.6 1.7 40 39-82 6-45 (55)
16 KOG3993|consensus 98.8 9.5E-10 2.1E-14 80.2 1.4 121 3-126 295-488 (500)
17 PHA02768 hypothetical protein; 98.8 2E-09 4.3E-14 57.1 1.1 38 69-108 6-43 (55)
18 PF13465 zf-H2C2_2: Zinc-finge 98.7 2.5E-08 5.3E-13 45.3 2.4 24 84-107 2-25 (26)
19 KOG3993|consensus 98.6 1.8E-08 3.9E-13 73.7 1.1 108 4-121 268-381 (500)
20 PF13465 zf-H2C2_2: Zinc-finge 98.6 6.4E-08 1.4E-12 43.9 2.3 25 55-79 1-25 (26)
21 PHA00616 hypothetical protein 98.4 1.4E-07 3.1E-12 47.6 1.7 32 96-127 1-32 (44)
22 PF00096 zf-C2H2: Zinc finger, 98.2 4.5E-07 9.7E-12 39.8 1.0 21 4-25 1-21 (23)
23 PHA00616 hypothetical protein 98.2 6E-07 1.3E-11 45.4 1.2 28 44-71 5-32 (44)
24 PHA00732 hypothetical protein 98.1 2.4E-06 5.2E-11 49.4 2.0 21 3-24 1-21 (79)
25 PHA00732 hypothetical protein 98.0 3.6E-06 7.8E-11 48.6 2.5 48 38-93 1-49 (79)
26 PF05605 zf-Di19: Drought indu 98.0 3.6E-06 7.9E-11 45.1 2.3 51 3-64 2-53 (54)
27 PF13894 zf-C2H2_4: C2H2-type 98.0 2.9E-06 6.3E-11 37.3 1.2 22 4-26 1-22 (24)
28 PF13912 zf-C2H2_6: C2H2-type 97.9 4.2E-06 9E-11 38.2 1.1 23 3-26 1-23 (27)
29 COG5189 SFP1 Putative transcri 97.9 2.5E-06 5.4E-11 60.7 -0.3 72 36-117 347-419 (423)
30 PF00096 zf-C2H2: Zinc finger, 97.8 2.2E-05 4.7E-10 34.2 2.3 23 39-63 1-23 (23)
31 PF05605 zf-Di19: Drought indu 97.8 5.5E-05 1.2E-09 40.5 4.2 49 69-120 3-53 (54)
32 PF13912 zf-C2H2_6: C2H2-type 97.7 3.1E-05 6.7E-10 35.2 2.1 25 96-120 1-25 (27)
33 PF13894 zf-C2H2_4: C2H2-type 97.7 5.2E-05 1.1E-09 33.1 2.6 24 97-120 1-24 (24)
34 COG5189 SFP1 Putative transcri 97.6 2.7E-05 5.9E-10 55.5 1.5 22 2-24 348-371 (423)
35 PF12756 zf-C2H2_2: C2H2 type 97.5 8.9E-05 1.9E-09 44.5 2.4 74 5-92 1-74 (100)
36 PF12756 zf-C2H2_2: C2H2 type 97.3 0.00025 5.4E-09 42.5 3.2 74 40-120 1-74 (100)
37 PF13913 zf-C2HC_2: zinc-finge 97.2 0.00018 3.9E-09 32.1 1.2 23 3-27 2-24 (25)
38 smart00355 ZnF_C2H2 zinc finge 97.2 0.00016 3.6E-09 32.0 0.9 20 5-25 2-21 (26)
39 PF12171 zf-C2H2_jaz: Zinc-fin 97.0 0.00017 3.6E-09 32.8 -0.0 21 4-25 2-22 (27)
40 smart00355 ZnF_C2H2 zinc finge 96.9 0.0011 2.4E-08 29.1 2.4 23 97-119 1-23 (26)
41 PF09237 GAGA: GAGA factor; I 96.8 0.00094 2E-08 34.7 1.9 30 36-67 22-51 (54)
42 PF13909 zf-H2C2_5: C2H2-type 96.8 0.0017 3.6E-08 28.4 2.5 24 97-121 1-24 (24)
43 PF09237 GAGA: GAGA factor; I 96.7 0.0042 9.1E-08 32.3 3.8 34 63-96 19-52 (54)
44 PF12874 zf-met: Zinc-finger o 96.7 0.0015 3.3E-08 28.8 2.0 23 97-119 1-23 (25)
45 PRK04860 hypothetical protein; 96.3 0.0042 9.1E-08 40.8 2.9 36 68-107 119-154 (160)
46 PF13719 zinc_ribbon_5: zinc-r 96.1 0.0041 8.8E-08 30.4 1.7 36 2-51 1-36 (37)
47 PF12874 zf-met: Zinc-finger o 96.1 0.0053 1.1E-07 27.0 1.9 19 4-23 1-19 (25)
48 PF13717 zinc_ribbon_4: zinc-r 95.9 0.0076 1.7E-07 29.3 2.1 36 2-51 1-36 (36)
49 PRK04860 hypothetical protein; 95.8 0.01 2.2E-07 39.1 3.0 39 37-81 118-156 (160)
50 TIGR02098 MJ0042_CXXC MJ0042 f 95.8 0.0069 1.5E-07 29.7 1.7 36 2-51 1-36 (38)
51 PF12171 zf-C2H2_jaz: Zinc-fin 95.5 0.0057 1.2E-07 27.6 0.6 22 39-62 2-23 (27)
52 PF13909 zf-H2C2_5: C2H2-type 95.3 0.021 4.5E-07 24.8 2.2 19 44-63 4-22 (24)
53 KOG2231|consensus 95.2 0.034 7.3E-07 44.3 4.4 67 50-120 159-236 (669)
54 KOG1146|consensus 94.8 0.0084 1.8E-07 50.6 0.1 58 2-62 464-540 (1406)
55 PRK00398 rpoP DNA-directed RNA 94.8 0.037 8E-07 28.4 2.5 32 1-51 1-32 (46)
56 smart00451 ZnF_U1 U1-like zinc 94.1 0.028 6.1E-07 26.7 1.1 21 3-24 3-23 (35)
57 KOG1146|consensus 93.9 0.017 3.6E-07 48.9 0.0 103 6-119 439-541 (1406)
58 smart00451 ZnF_U1 U1-like zinc 93.5 0.092 2E-06 24.9 2.3 24 96-119 3-26 (35)
59 COG4049 Uncharacterized protei 93.4 0.033 7.2E-07 29.5 0.7 23 2-25 16-38 (65)
60 COG5048 FOG: Zn-finger [Genera 93.0 0.045 9.7E-07 41.0 1.1 62 3-71 289-354 (467)
61 TIGR00622 ssl1 transcription f 92.6 0.22 4.7E-06 30.7 3.4 24 96-119 81-104 (112)
62 KOG2785|consensus 92.1 0.39 8.5E-06 35.7 4.8 51 68-118 166-242 (390)
63 COG2888 Predicted Zn-ribbon RN 91.6 0.11 2.3E-06 28.0 1.1 33 37-76 26-58 (61)
64 KOG2186|consensus 90.8 0.27 5.8E-06 34.6 2.8 49 1-61 1-49 (276)
65 cd00350 rubredoxin_like Rubred 90.8 0.18 4E-06 23.8 1.4 8 96-103 17-24 (33)
66 PF12013 DUF3505: Protein of u 90.6 1.2 2.6E-05 27.2 5.4 23 2-26 10-32 (109)
67 PF09986 DUF2225: Uncharacteri 90.0 0.12 2.5E-06 35.8 0.5 49 2-53 4-61 (214)
68 COG5048 FOG: Zn-finger [Genera 89.8 0.093 2E-06 39.3 -0.1 60 68-127 289-354 (467)
69 KOG4173|consensus 89.4 0.14 3E-06 34.9 0.5 80 38-120 79-170 (253)
70 smart00531 TFIIE Transcription 89.0 0.35 7.6E-06 31.4 2.2 41 34-80 95-135 (147)
71 PF09538 FYDLN_acid: Protein o 88.9 0.43 9.4E-06 29.3 2.4 30 39-81 10-39 (108)
72 PF09723 Zn-ribbon_8: Zinc rib 88.5 0.33 7.1E-06 24.3 1.4 14 4-17 6-19 (42)
73 KOG2186|consensus 88.4 0.31 6.8E-06 34.2 1.7 49 39-92 4-52 (276)
74 PF07754 DUF1610: Domain of un 88.3 0.31 6.6E-06 21.3 1.0 10 2-11 15-24 (24)
75 KOG2893|consensus 88.0 0.14 3.1E-06 35.6 -0.1 41 6-59 13-53 (341)
76 KOG2482|consensus 87.6 1.5 3.3E-05 32.4 4.8 51 69-119 280-357 (423)
77 COG5236 Uncharacterized conser 87.3 0.38 8.2E-06 35.5 1.6 27 39-65 152-178 (493)
78 smart00834 CxxC_CXXC_SSSS Puta 87.1 0.49 1.1E-05 23.2 1.6 15 3-17 5-19 (41)
79 KOG4167|consensus 87.0 0.14 3E-06 41.2 -0.8 25 3-28 792-816 (907)
80 KOG2231|consensus 86.6 1.5 3.2E-05 35.4 4.6 69 39-117 183-260 (669)
81 KOG2893|consensus 86.1 0.19 4.2E-06 35.0 -0.3 39 45-87 15-53 (341)
82 COG4049 Uncharacterized protei 85.7 0.56 1.2E-05 24.9 1.3 29 92-120 13-41 (65)
83 TIGR00622 ssl1 transcription f 85.6 1.3 2.7E-05 27.4 3.0 83 3-92 15-105 (112)
84 TIGR01206 lysW lysine biosynth 85.5 0.83 1.8E-05 24.3 2.0 32 2-50 1-32 (54)
85 smart00440 ZnF_C2C2 C2C2 Zinc 85.4 0.42 9.1E-06 23.7 0.8 39 4-51 1-39 (40)
86 PRK14890 putative Zn-ribbon RN 84.5 0.58 1.3E-05 25.3 1.1 34 36-76 23-56 (59)
87 PF05443 ROS_MUCR: ROS/MUCR tr 83.9 0.7 1.5E-05 29.4 1.5 23 4-30 73-95 (132)
88 PF08209 Sgf11: Sgf11 (transcr 83.7 1.5 3.2E-05 20.8 2.2 26 2-29 3-28 (33)
89 PRK09678 DNA-binding transcrip 83.3 0.46 1E-05 26.9 0.4 44 4-56 2-45 (72)
90 PF01096 TFIIS_C: Transcriptio 82.7 0.25 5.3E-06 24.4 -0.7 38 4-50 1-38 (39)
91 COG4957 Predicted transcriptio 82.7 1.2 2.5E-05 28.4 2.0 23 4-30 77-99 (148)
92 TIGR00373 conserved hypothetic 82.6 0.48 1E-05 31.2 0.4 34 35-79 106-139 (158)
93 PRK06266 transcription initiat 82.6 0.53 1.1E-05 31.6 0.6 32 37-79 116-147 (178)
94 TIGR02605 CxxC_CxxC_SSSS putat 82.5 0.93 2E-05 23.6 1.4 12 4-15 6-17 (52)
95 smart00734 ZnF_Rad18 Rad18-lik 82.2 0.77 1.7E-05 20.4 0.9 19 4-24 2-20 (26)
96 PF15269 zf-C2H2_7: Zinc-finge 81.5 0.85 1.8E-05 23.1 1.0 22 4-26 21-42 (54)
97 TIGR02300 FYDLN_acid conserved 81.1 1.3 2.8E-05 27.9 1.9 33 38-83 9-41 (129)
98 COG1996 RPC10 DNA-directed RNA 80.5 0.75 1.6E-05 23.9 0.6 13 1-13 4-16 (49)
99 cd00729 rubredoxin_SM Rubredox 79.8 1.3 2.8E-05 21.0 1.3 8 96-103 18-25 (34)
100 PHA00626 hypothetical protein 79.6 1.8 3.9E-05 23.1 1.8 14 37-52 22-35 (59)
101 PRK00464 nrdR transcriptional 78.9 0.78 1.7E-05 30.0 0.4 17 38-56 28-44 (154)
102 TIGR00373 conserved hypothetic 78.5 1.9 4.2E-05 28.3 2.2 34 63-105 104-137 (158)
103 PF08790 zf-LYAR: LYAR-type C2 78.0 0.83 1.8E-05 20.7 0.2 18 4-23 1-18 (28)
104 PF06397 Desulfoferrod_N: Desu 78.0 1.3 2.9E-05 21.4 1.0 13 2-14 5-17 (36)
105 KOG2785|consensus 77.9 2.3 5.1E-05 31.8 2.6 57 3-62 166-242 (390)
106 COG1592 Rubrerythrin [Energy p 77.8 1.9 4E-05 28.7 1.9 24 68-104 134-157 (166)
107 smart00531 TFIIE Transcription 77.0 5.6 0.00012 25.8 4.0 38 65-106 96-133 (147)
108 COG3364 Zn-ribbon containing p 77.0 1.2 2.7E-05 26.8 0.9 16 2-17 1-16 (112)
109 smart00659 RPOLCX RNA polymera 76.8 1.6 3.4E-05 22.1 1.1 14 2-15 1-14 (44)
110 PF04606 Ogr_Delta: Ogr/Delta- 75.5 1.4 3E-05 22.6 0.7 40 5-53 1-40 (47)
111 KOG4173|consensus 74.7 0.97 2.1E-05 30.9 0.0 73 4-88 80-166 (253)
112 PRK06266 transcription initiat 74.4 3.2 6.9E-05 27.9 2.4 33 65-106 114-146 (178)
113 COG1997 RPL43A Ribosomal prote 73.4 2.4 5.3E-05 24.8 1.4 11 69-79 54-64 (89)
114 PF02892 zf-BED: BED zinc fing 73.2 4.3 9.3E-05 20.2 2.2 22 3-24 16-40 (45)
115 PF10571 UPF0547: Uncharacteri 71.8 2 4.4E-05 19.1 0.7 10 5-14 16-25 (26)
116 PF03884 DUF329: Domain of unk 71.5 2.1 4.6E-05 23.0 0.9 14 2-15 1-14 (57)
117 COG2331 Uncharacterized protei 70.7 2.1 4.4E-05 24.4 0.7 10 4-13 13-22 (82)
118 PF05191 ADK_lid: Adenylate ki 70.4 3 6.5E-05 20.1 1.2 14 4-17 2-15 (36)
119 PF12013 DUF3505: Protein of u 70.4 4.8 0.0001 24.5 2.4 25 97-121 81-109 (109)
120 smart00154 ZnF_AN1 AN1-like Zi 70.2 2.4 5.1E-05 20.8 0.8 14 3-16 12-25 (39)
121 PF01428 zf-AN1: AN1-like Zinc 70.2 1.9 4.1E-05 21.6 0.5 13 3-15 13-25 (43)
122 PF13878 zf-C2H2_3: zinc-finge 70.2 4.2 9E-05 20.2 1.7 23 4-26 14-37 (41)
123 cd00974 DSRD Desulforedoxin (D 69.2 3.3 7.1E-05 19.5 1.2 13 2-14 3-15 (34)
124 PF09845 DUF2072: Zn-ribbon co 68.7 2.8 6E-05 26.6 1.0 15 3-17 1-15 (131)
125 smart00614 ZnF_BED BED zinc fi 68.5 4.4 9.6E-05 20.9 1.7 22 4-25 19-44 (50)
126 COG4311 SoxD Sarcosine oxidase 67.7 2.7 5.9E-05 24.9 0.8 12 1-12 1-12 (97)
127 COG5236 Uncharacterized conser 66.9 15 0.00033 27.5 4.6 74 40-120 222-305 (493)
128 TIGR00319 desulf_FeS4 desulfof 66.5 4 8.7E-05 19.2 1.2 13 2-14 6-18 (34)
129 PRK03824 hypA hydrogenase nick 66.3 4.4 9.5E-05 25.9 1.7 13 3-15 70-82 (135)
130 COG1594 RPB9 DNA-directed RNA 66.3 3.5 7.6E-05 25.5 1.2 12 38-51 100-111 (113)
131 PF13451 zf-trcl: Probable zin 65.7 3.7 8.1E-05 21.3 1.0 16 2-17 3-18 (49)
132 PLN03238 probable histone acet 64.5 8.6 0.00019 27.9 2.9 37 2-40 47-83 (290)
133 COG5188 PRP9 Splicing factor 3 64.2 7.9 0.00017 28.9 2.7 31 88-118 366-397 (470)
134 KOG3408|consensus 64.0 3.3 7.3E-05 25.8 0.7 23 3-26 57-79 (129)
135 PF12760 Zn_Tnp_IS1595: Transp 63.5 5.6 0.00012 20.1 1.4 9 67-75 36-44 (46)
136 PF14353 CpXC: CpXC protein 63.4 2 4.4E-05 27.0 -0.3 20 3-23 38-57 (128)
137 PF04959 ARS2: Arsenite-resist 62.0 4.5 9.7E-05 28.1 1.2 32 32-65 71-102 (214)
138 PF02176 zf-TRAF: TRAF-type zi 61.3 18 0.00039 19.1 3.3 18 84-101 26-43 (60)
139 PF03811 Zn_Tnp_IS1: InsA N-te 60.4 6.3 0.00014 19.0 1.2 31 3-46 5-35 (36)
140 PF09963 DUF2197: Uncharacteri 60.2 5.1 0.00011 21.4 0.9 41 2-50 1-41 (56)
141 PF04959 ARS2: Arsenite-resist 60.1 5.6 0.00012 27.6 1.3 29 94-122 75-103 (214)
142 PF07975 C1_4: TFIIH C1-like d 58.4 4.1 8.9E-05 21.4 0.4 20 68-87 21-40 (51)
143 smart00661 RPOL9 RNA polymeras 56.9 11 0.00025 19.2 2.0 13 38-52 20-32 (52)
144 PF10013 DUF2256: Uncharacteri 56.5 5 0.00011 20.1 0.5 13 5-17 10-22 (42)
145 PF10276 zf-CHCC: Zinc-finger 56.1 6.4 0.00014 19.5 0.8 11 3-13 29-39 (40)
146 PF12907 zf-met2: Zinc-binding 56.0 3.8 8.3E-05 20.3 0.0 21 4-24 2-24 (40)
147 KOG2807|consensus 55.3 28 0.0006 25.9 4.2 25 95-119 344-368 (378)
148 PTZ00064 histone acetyltransfe 54.8 15 0.00032 29.0 2.9 38 2-41 279-316 (552)
149 PF14803 Nudix_N_2: Nudix N-te 54.6 9.6 0.00021 18.1 1.3 13 36-50 20-32 (34)
150 KOG3408|consensus 54.4 9.5 0.00021 23.9 1.5 27 93-119 54-80 (129)
151 PF04423 Rad50_zn_hook: Rad50 54.2 5.5 0.00012 20.9 0.5 13 5-17 22-34 (54)
152 PF06524 NOA36: NOA36 protein; 53.1 5.3 0.00011 28.5 0.3 84 34-120 138-233 (314)
153 PLN00104 MYST -like histone ac 52.8 15 0.00033 28.5 2.7 38 2-41 197-234 (450)
154 PF08271 TF_Zn_Ribbon: TFIIB z 52.4 13 0.00029 18.4 1.7 10 4-13 1-10 (43)
155 TIGR01384 TFS_arch transcripti 52.0 5.8 0.00012 23.9 0.4 11 68-78 90-100 (104)
156 KOG2593|consensus 51.8 10 0.00022 29.1 1.6 39 35-78 125-163 (436)
157 PHA02998 RNA polymerase subuni 50.6 7.5 0.00016 26.1 0.7 11 39-51 172-182 (195)
158 KOG2907|consensus 50.2 13 0.00028 23.0 1.6 10 69-78 103-112 (116)
159 PF12230 PRP21_like_P: Pre-mRN 49.4 5.5 0.00012 27.8 0.0 22 3-26 168-189 (229)
160 KOG2482|consensus 49.1 16 0.00034 27.3 2.2 24 97-120 280-303 (423)
161 PRK00432 30S ribosomal protein 48.9 15 0.00033 19.1 1.6 11 38-50 37-47 (50)
162 PF03604 DNA_RNApol_7kD: DNA d 48.6 9.1 0.0002 17.9 0.7 11 4-14 1-11 (32)
163 PF05129 Elf1: Transcription e 47.8 7.5 0.00016 22.5 0.4 11 69-79 47-57 (81)
164 PF05290 Baculo_IE-1: Baculovi 47.0 19 0.00041 23.0 2.0 17 34-52 76-92 (140)
165 COG4530 Uncharacterized protei 45.5 14 0.0003 22.7 1.3 26 44-80 13-38 (129)
166 PF08792 A2L_zn_ribbon: A2L zi 45.5 12 0.00027 17.6 0.9 11 4-14 22-32 (33)
167 KOG4167|consensus 45.4 5.2 0.00011 32.8 -0.7 27 37-65 791-817 (907)
168 PF05495 zf-CHY: CHY zinc fing 45.1 5 0.00011 22.5 -0.6 13 68-80 41-53 (71)
169 KOG2747|consensus 45.0 19 0.0004 27.5 2.1 36 2-39 157-192 (396)
170 COG3024 Uncharacterized protei 44.9 10 0.00022 20.9 0.6 11 4-14 8-18 (65)
171 PF14354 Lar_restr_allev: Rest 44.9 9.5 0.00021 20.4 0.5 14 2-15 2-15 (61)
172 PF04438 zf-HIT: HIT zinc fing 44.5 12 0.00025 17.2 0.7 11 3-13 13-23 (30)
173 KOG0717|consensus 44.2 11 0.00023 29.3 0.8 23 97-119 461-483 (508)
174 PF08274 PhnA_Zn_Ribbon: PhnA 44.1 11 0.00024 17.4 0.5 9 3-11 19-27 (30)
175 PF01286 XPA_N: XPA protein N- 44.0 11 0.00023 18.0 0.5 13 5-17 5-17 (34)
176 PF11672 DUF3268: Protein of u 44.0 19 0.0004 21.9 1.7 15 2-16 1-15 (102)
177 PF07800 DUF1644: Protein of u 43.7 95 0.0021 20.6 5.2 57 69-127 81-140 (162)
178 KOG1842|consensus 42.5 9.4 0.0002 29.5 0.3 22 4-26 16-37 (505)
179 PF00301 Rubredoxin: Rubredoxi 42.3 23 0.00049 18.2 1.6 14 4-17 2-15 (47)
180 COG5151 SSL1 RNA polymerase II 41.8 13 0.00029 27.3 0.9 48 70-119 364-411 (421)
181 COG1571 Predicted DNA-binding 41.5 17 0.00036 28.0 1.4 15 38-54 367-381 (421)
182 COG0068 HypF Hydrogenase matur 41.4 5.4 0.00012 32.6 -1.1 58 3-75 122-180 (750)
183 PTZ00043 cytochrome c oxidase 41.0 11 0.00024 26.4 0.4 16 2-17 180-195 (268)
184 PLN03239 histone acetyltransfe 40.7 34 0.00074 25.7 2.9 39 2-41 105-145 (351)
185 PF14446 Prok-RING_1: Prokaryo 40.3 13 0.00027 19.8 0.5 13 5-17 7-19 (54)
186 PRK03564 formate dehydrogenase 40.1 18 0.00038 26.7 1.4 10 95-104 251-260 (309)
187 PF13453 zf-TFIIB: Transcripti 39.9 20 0.00043 17.5 1.2 13 44-56 23-35 (41)
188 COG5216 Uncharacterized conser 39.9 13 0.00029 20.0 0.5 11 65-75 41-51 (67)
189 KOG2593|consensus 39.6 36 0.00079 26.2 2.9 38 64-104 124-161 (436)
190 KOG2272|consensus 38.9 13 0.00028 26.5 0.5 13 95-107 220-232 (332)
191 PF04216 FdhE: Protein involve 38.4 5.1 0.00011 29.1 -1.6 35 69-104 212-246 (290)
192 PTZ00448 hypothetical protein; 38.2 17 0.00037 27.4 1.1 19 44-62 318-336 (373)
193 PF11789 zf-Nse: Zinc-finger o 38.0 62 0.0013 17.2 3.0 9 44-52 28-36 (57)
194 PRK00418 DNA gyrase inhibitor; 37.8 15 0.00032 20.1 0.5 10 4-13 7-16 (62)
195 cd00730 rubredoxin Rubredoxin; 37.6 22 0.00049 18.5 1.2 12 4-15 2-13 (50)
196 COG1198 PriA Primosomal protei 37.1 22 0.00049 29.5 1.7 11 67-77 474-484 (730)
197 COG4338 Uncharacterized protei 36.8 10 0.00023 19.5 -0.1 12 5-16 14-25 (54)
198 TIGR00320 dfx_rbo desulfoferro 36.5 21 0.00046 22.5 1.2 13 2-14 6-18 (125)
199 PF13248 zf-ribbon_3: zinc-rib 36.5 14 0.0003 16.1 0.2 7 5-11 4-10 (26)
200 COG3677 Transposase and inacti 36.4 27 0.0006 22.1 1.7 14 37-52 52-65 (129)
201 KOG0717|consensus 36.4 17 0.00037 28.3 0.8 24 4-28 461-484 (508)
202 COG5027 SAS2 Histone acetyltra 36.4 33 0.00072 25.8 2.2 29 1-30 156-184 (395)
203 COG1773 Rubredoxin [Energy pro 36.2 20 0.00044 19.1 0.9 17 1-17 1-17 (55)
204 PF04780 DUF629: Protein of un 35.8 20 0.00044 28.0 1.2 21 5-26 59-79 (466)
205 PF15616 TerY-C: TerY-C metal 34.2 22 0.00047 22.7 0.9 11 68-78 105-115 (131)
206 PRK01343 zinc-binding protein; 34.0 19 0.00041 19.4 0.6 11 4-14 10-20 (57)
207 PF14255 Cys_rich_CPXG: Cystei 33.8 17 0.00036 19.2 0.3 11 5-15 2-12 (52)
208 TIGR03831 YgiT_finger YgiT-typ 33.6 20 0.00044 17.6 0.6 12 4-15 33-44 (46)
209 PF14787 zf-CCHC_5: GAG-polypr 33.4 19 0.00042 17.3 0.5 11 5-15 4-14 (36)
210 PF01780 Ribosomal_L37ae: Ribo 33.1 21 0.00045 21.2 0.7 10 3-12 35-44 (90)
211 PF10083 DUF2321: Uncharacteri 32.9 18 0.00039 23.8 0.4 27 92-118 64-90 (158)
212 PF01194 RNA_pol_N: RNA polyme 32.7 17 0.00037 19.8 0.2 16 2-17 3-18 (60)
213 TIGR00686 phnA alkylphosphonat 32.1 32 0.0007 21.1 1.4 30 5-54 4-33 (109)
214 KOG1280|consensus 31.9 47 0.001 25.0 2.4 21 3-24 79-99 (381)
215 PRK10220 hypothetical protein; 31.9 39 0.00086 20.8 1.7 33 2-54 2-34 (111)
216 PF14447 Prok-RING_4: Prokaryo 31.6 22 0.00048 18.9 0.6 10 6-15 42-51 (55)
217 PF06220 zf-U1: U1 zinc finger 31.5 34 0.00073 16.6 1.2 12 2-13 2-13 (38)
218 KOG4124|consensus 31.3 6.3 0.00014 29.4 -2.0 71 36-115 347-417 (442)
219 PF07282 OrfB_Zn_ribbon: Putat 31.2 39 0.00084 18.4 1.6 12 95-106 45-56 (69)
220 PRK14714 DNA polymerase II lar 31.0 72 0.0016 28.5 3.6 9 4-12 668-676 (1337)
221 PF13824 zf-Mss51: Zinc-finger 30.8 46 0.00099 17.8 1.7 14 93-106 11-24 (55)
222 KOG3497|consensus 30.8 26 0.00055 19.1 0.7 16 2-17 3-18 (69)
223 KOG3507|consensus 30.3 29 0.00062 18.8 0.9 10 2-11 19-28 (62)
224 PF08782 c-SKI_SMAD_bind: c-SK 29.8 21 0.00045 21.4 0.3 18 4-23 29-46 (96)
225 COG1885 Uncharacterized protei 29.5 23 0.00051 21.5 0.5 12 4-15 50-61 (115)
226 KOG1280|consensus 29.5 76 0.0016 23.9 3.1 24 36-61 77-100 (381)
227 COG3091 SprT Zn-dependent meta 29.3 36 0.00078 22.3 1.3 8 96-103 140-147 (156)
228 PF13240 zinc_ribbon_2: zinc-r 29.3 19 0.00041 15.3 0.1 6 6-11 16-21 (23)
229 PF05180 zf-DNL: DNL zinc fing 29.0 19 0.00041 20.0 0.1 38 2-51 3-40 (66)
230 PF04780 DUF629: Protein of un 29.0 52 0.0011 25.8 2.4 24 97-120 58-81 (466)
231 PF14369 zf-RING_3: zinc-finge 28.4 27 0.00058 16.6 0.5 10 5-14 23-32 (35)
232 PF07649 C1_3: C1-like domain; 28.2 34 0.00074 15.3 0.9 12 2-13 14-25 (30)
233 PF09855 DUF2082: Nucleic-acid 28.1 23 0.00051 19.5 0.3 9 4-12 1-9 (64)
234 TIGR03655 anti_R_Lar restricti 28.0 22 0.00047 18.5 0.2 12 39-52 27-38 (53)
235 PF11931 DUF3449: Domain of un 27.6 20 0.00044 24.6 0.0 23 2-24 100-122 (196)
236 PF01927 Mut7-C: Mut7-C RNAse 27.5 44 0.00096 21.6 1.6 46 38-85 91-141 (147)
237 PF05741 zf-nanos: Nanos RNA b 27.5 21 0.00045 19.1 0.0 10 3-12 33-42 (55)
238 COG3809 Uncharacterized protei 27.0 76 0.0017 18.3 2.2 27 34-62 17-43 (88)
239 PRK14892 putative transcriptio 26.9 82 0.0018 19.0 2.5 12 69-80 43-54 (99)
240 PF06827 zf-FPG_IleRS: Zinc fi 26.8 29 0.00063 15.5 0.5 11 5-15 3-13 (30)
241 COG4888 Uncharacterized Zn rib 26.6 26 0.00057 21.2 0.4 40 35-80 19-58 (104)
242 PF14375 Cys_rich_CWC: Cystein 26.6 31 0.00068 17.8 0.6 6 7-12 2-7 (50)
243 KOG2636|consensus 26.5 61 0.0013 25.3 2.3 32 88-119 393-425 (497)
244 PF01363 FYVE: FYVE zinc finge 26.0 16 0.00034 20.0 -0.7 10 5-14 11-20 (69)
245 PF08882 Acetone_carb_G: Aceto 26.0 37 0.00079 21.0 0.9 10 69-78 75-84 (112)
246 PRK08222 hydrogenase 4 subunit 25.7 34 0.00074 23.0 0.8 13 4-16 115-127 (181)
247 KOG0978|consensus 25.4 12 0.00025 30.8 -1.7 16 70-85 680-695 (698)
248 PRK12496 hypothetical protein; 25.3 55 0.0012 21.7 1.7 12 39-52 128-139 (164)
249 COG1655 Uncharacterized protei 25.0 32 0.0007 24.3 0.6 16 2-17 18-33 (267)
250 TIGR00280 L37a ribosomal prote 24.9 33 0.00072 20.4 0.6 14 37-52 52-65 (91)
251 PF13408 Zn_ribbon_recom: Reco 24.8 37 0.00081 17.5 0.7 13 3-15 5-17 (58)
252 TIGR00100 hypA hydrogenase nic 24.7 43 0.00092 20.7 1.1 12 39-52 71-82 (115)
253 PRK04016 DNA-directed RNA poly 24.7 36 0.00078 18.6 0.6 17 1-17 2-18 (62)
254 PF14952 zf-tcix: Putative tre 24.4 32 0.00069 17.4 0.4 8 5-12 13-20 (44)
255 PF05876 Terminase_GpA: Phage 24.3 43 0.00092 26.9 1.2 43 4-54 201-243 (557)
256 KOG1729|consensus 24.2 47 0.001 24.3 1.4 24 4-28 169-192 (288)
257 PF11781 RRN7: RNA polymerase 24.0 32 0.00068 16.5 0.3 12 4-15 9-20 (36)
258 PRK12380 hydrogenase nickel in 23.8 56 0.0012 20.2 1.5 12 39-52 71-82 (113)
259 TIGR00595 priA primosomal prot 23.6 31 0.00067 27.3 0.4 9 96-104 253-261 (505)
260 PRK00564 hypA hydrogenase nick 23.6 36 0.00077 21.1 0.6 14 3-16 71-84 (117)
261 PF14690 zf-ISL3: zinc-finger 23.5 32 0.00069 17.1 0.3 8 3-10 2-9 (47)
262 PTZ00255 60S ribosomal protein 23.5 36 0.00078 20.2 0.5 14 37-52 53-66 (90)
263 COG1675 TFA1 Transcription ini 23.4 40 0.00088 22.7 0.8 34 35-79 110-143 (176)
264 TIGR00515 accD acetyl-CoA carb 23.4 40 0.00086 24.6 0.8 9 5-13 28-36 (285)
265 PLN00032 DNA-directed RNA poly 23.3 40 0.00086 19.0 0.6 23 1-23 2-24 (71)
266 COG3357 Predicted transcriptio 23.2 29 0.00064 20.6 0.1 9 44-52 62-70 (97)
267 PF11023 DUF2614: Protein of u 22.9 49 0.0011 20.5 1.0 13 3-15 69-81 (114)
268 PF01844 HNH: HNH endonuclease 22.7 14 0.0003 18.3 -1.2 17 6-23 1-17 (47)
269 PRK03976 rpl37ae 50S ribosomal 22.7 39 0.00084 20.1 0.6 13 38-52 54-66 (90)
270 PF03145 Sina: Seven in absent 22.4 82 0.0018 21.3 2.2 55 2-66 13-73 (198)
271 smart00132 LIM Zinc-binding do 22.1 36 0.00078 15.6 0.3 10 4-13 28-37 (39)
272 COG4896 Uncharacterized protei 21.9 52 0.0011 18.0 0.9 11 37-49 30-40 (68)
273 COG1998 RPS31 Ribosomal protei 21.8 79 0.0017 16.5 1.5 8 39-48 38-45 (51)
274 COG2879 Uncharacterized small 21.7 1.1E+02 0.0023 16.9 2.1 19 107-125 23-41 (65)
275 PTZ00448 hypothetical protein; 21.1 77 0.0017 24.1 1.9 23 96-118 314-336 (373)
276 PF04267 SoxD: Sarcosine oxida 21.0 49 0.0011 19.4 0.7 10 3-12 1-10 (84)
277 KOG2703|consensus 20.8 48 0.001 25.5 0.8 11 2-12 67-77 (460)
278 PF14205 Cys_rich_KTR: Cystein 20.3 89 0.0019 16.6 1.6 32 4-48 5-36 (55)
279 PF10058 DUF2296: Predicted in 20.2 1.4E+02 0.003 15.8 2.3 8 68-75 44-51 (54)
280 PRK05978 hypothetical protein; 20.0 45 0.00097 21.8 0.5 7 6-12 36-42 (148)
No 1
>KOG2462|consensus
Probab=99.94 E-value=6.4e-27 Score=160.02 Aligned_cols=121 Identities=26% Similarity=0.487 Sum_probs=107.9
Q ss_pred eeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChH
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQS 82 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~ 82 (151)
.|+|++||+.+.+.. +|-.|.-+|-.+ ...+-+.| +.|++.|.+-.+|+.|+++|. .+.+|.+||+.|.++.
T Consensus 130 r~~c~eCgk~ysT~s-nLsrHkQ~H~~~---~s~ka~~C--~~C~K~YvSmpALkMHirTH~--l~c~C~iCGKaFSRPW 201 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSS-NLSRHKQTHRSL---DSKKAFSC--KYCGKVYVSMPALKMHIRTHT--LPCECGICGKAFSRPW 201 (279)
T ss_pred ceecccccccccccc-ccchhhcccccc---cccccccC--CCCCceeeehHHHhhHhhccC--CCcccccccccccchH
Confidence 588999999999999 999994443322 22566889 999999999999999999997 5789999999999999
Q ss_pred HHHHHHhhhCCCCceeCCcCCccccCHHHHHHHHhhhcCCcccccccCC
Q psy4404 83 ALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLKHNADLSSMIKLP 131 (151)
Q Consensus 83 ~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~~~~~ 131 (151)
.|+.|+++|+|||||.|+.|++.|..+++|+.||++|.+.+.|+|..|.
T Consensus 202 LLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~ 250 (279)
T KOG2462|consen 202 LLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCG 250 (279)
T ss_pred HhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchh
Confidence 9999999999999999999999999999999999999999999997764
No 2
>KOG2462|consensus
Probab=99.92 E-value=6e-26 Score=155.27 Aligned_cols=107 Identities=29% Similarity=0.541 Sum_probs=99.8
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCCh
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQ 81 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 81 (151)
+.+.|+.|||.|-+.. +|.+| .++|+ .++.| +.||+.|....-|+.|+|+|+|++||.|+.|+++|...
T Consensus 160 ka~~C~~C~K~YvSmp-ALkMH------irTH~--l~c~C--~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADR 228 (279)
T KOG2462|consen 160 KAFSCKYCGKVYVSMP-ALKMH------IRTHT--LPCEC--GICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADR 228 (279)
T ss_pred ccccCCCCCceeeehH-HHhhH------hhccC--CCccc--ccccccccchHHhhcccccccCCCCccCCcccchhcch
Confidence 4688999999999999 99999 45565 56788 99999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhCCCCceeCCcCCccccCHHHHHHHHhhh
Q psy4404 82 SALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 82 ~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
++|..|+.+|.+.++|.|..|++.|...+.|.+|...-
T Consensus 229 SNLRAHmQTHS~~K~~qC~~C~KsFsl~SyLnKH~ES~ 266 (279)
T KOG2462|consen 229 SNLRAHMQTHSDVKKHQCPRCGKSFALKSYLNKHSESA 266 (279)
T ss_pred HHHHHHHHhhcCCccccCcchhhHHHHHHHHHHhhhhc
Confidence 99999999999999999999999999999999997643
No 3
>KOG3576|consensus
Probab=99.70 E-value=4.5e-18 Score=112.12 Aligned_cols=116 Identities=26% Similarity=0.474 Sum_probs=102.0
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCCh
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQ 81 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 81 (151)
.+|.|..|||.|.... .|..| ++-|...+.+-| ..||+.|.+.-.|.+|+++|++.+||.|..|+++|...
T Consensus 116 d~ftCrvCgK~F~lQR-mlnrh------~kch~~vkr~lc--t~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqr 186 (267)
T KOG3576|consen 116 DSFTCRVCGKKFGLQR-MLNRH------LKCHSDVKRHLC--TFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQR 186 (267)
T ss_pred CeeeeehhhhhhhHHH-HHHHH------hhhccHHHHHHH--hhccCcccchhhhhhhhccccCccccchhhhhHHHHhh
Confidence 3689999999999999 99999 566888888999 88999999999999999999999999999999999999
Q ss_pred HHHHHHHhh-hC----------CCCceeCCcCCccccCHHHHHHHHhhhcCCcccc
Q psy4404 82 SALYNHLKR-HT----------GEKPFKCTICSHKAARKDHMKRHLQLKHNADLSS 126 (151)
Q Consensus 82 ~~l~~h~~~-h~----------~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 126 (151)
-.|..|++. |. .++-|.|..||..-.....+..|++.++..-+..
T Consensus 187 csleshl~kvhgv~~~yaykerr~kl~vcedcg~t~~~~e~~~~h~~~~hp~Spal 242 (267)
T KOG3576|consen 187 CSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYTSERPEVYYLHLKLHHPFSPAL 242 (267)
T ss_pred ccHHHHHHHHcCchHHHHHHHhhhheeeecccCCCCCChhHHHHHHHhcCCCCHHH
Confidence 999998754 32 2466999999999999999999999998655543
No 4
>KOG1074|consensus
Probab=99.70 E-value=3.2e-18 Score=131.86 Aligned_cols=53 Identities=38% Similarity=0.677 Sum_probs=50.4
Q ss_pred eeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHHHHHhhhcC
Q psy4404 69 FHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLKHN 121 (151)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 121 (151)
-+|.+|.+++.....|+.|.++|+|++||+|.+|++.|..+.+|+.|+-+|.-
T Consensus 606 NqCiiC~rVlSC~saLqmHyrtHtGERPFkCKiCgRAFtTkGNLkaH~~vHka 658 (958)
T KOG1074|consen 606 NQCIICLRVLSCPSALQMHYRTHTGERPFKCKICGRAFTTKGNLKAHMSVHKA 658 (958)
T ss_pred cceeeeeecccchhhhhhhhhcccCcCccccccccchhccccchhhccccccc
Confidence 47999999999999999999999999999999999999999999999998863
No 5
>KOG3608|consensus
Probab=99.63 E-value=2.4e-16 Score=111.67 Aligned_cols=117 Identities=24% Similarity=0.625 Sum_probs=100.6
Q ss_pred CceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCC
Q psy4404 1 MILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQ 80 (151)
Q Consensus 1 ~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 80 (151)
.|+..||.||..|+++. .|..|++. .+.....+|.| ..|.+.|.+...|..|+..|.. .|+|+.|......
T Consensus 205 eKvvACp~Cg~~F~~~t-kl~DH~rR----qt~l~~n~fqC--~~C~KrFaTeklL~~Hv~rHvn--~ykCplCdmtc~~ 275 (467)
T KOG3608|consen 205 EKVVACPHCGELFRTKT-KLFDHLRR----QTELNTNSFQC--AQCFKRFATEKLLKSHVVRHVN--CYKCPLCDMTCSS 275 (467)
T ss_pred CeEEecchHHHHhcccc-HHHHHHHh----hhhhcCCchHH--HHHHHHHhHHHHHHHHHHHhhh--cccccccccCCCC
Confidence 37889999999999999 99999754 33345678999 8999999999999999998865 5899999999999
Q ss_pred hHHHHHHHhh-hCCCCceeCCcCCccccCHHHHHHHHhhhcCCccccc
Q psy4404 81 QSALYNHLKR-HTGEKPFKCTICSHKAARKDHMKRHLQLKHNADLSSM 127 (151)
Q Consensus 81 ~~~l~~h~~~-h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~ 127 (151)
.+.|..|++. |...+||+|..|++.+...+.|.+|...|. +..|.|
T Consensus 276 ~ssL~~H~r~rHs~dkpfKCd~Cd~~c~~esdL~kH~~~HS-~~~y~C 322 (467)
T KOG3608|consen 276 ASSLTTHIRYRHSKDKPFKCDECDTRCVRESDLAKHVQVHS-KTVYQC 322 (467)
T ss_pred hHHHHHHHHhhhccCCCccccchhhhhccHHHHHHHHHhcc-ccceec
Confidence 9999999865 788899999999999999999999998775 666666
No 6
>KOG3623|consensus
Probab=99.60 E-value=1.5e-16 Score=121.48 Aligned_cols=109 Identities=28% Similarity=0.625 Sum_probs=95.7
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCC-CcceeeccCCCCcccCCchHHHHHHHhhcCC-------------C
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDV-SFKYVCLYQKCSYHTGNSDHMRRHIRRHTGE-------------K 67 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~-~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~-------------~ 67 (151)
++..|+.|++.++... .|+.|+++ +|.. +.-|.| ..|..+|..+..|.+|+.+|... +
T Consensus 209 qlltcpycdrgykrlt-slkeHiky-----rhekne~nfsC--~lCsytFAyRtQLErhm~~hkpg~dqa~sltqsa~lR 280 (1007)
T KOG3623|consen 209 QLLTCPYCDRGYKRLT-SLKEHIKY-----RHEKNEPNFSC--MLCSYTFAYRTQLERHMQLHKPGGDQAISLTQSALLR 280 (1007)
T ss_pred hhhcchhHHHHHHHHH-HHHHHHHH-----HHhhCCCCCcc--hhhhhhhhhHHHHHHHHHhhcCCCcccccccchhhhc
Confidence 4678999999999999 99999865 3333 345889 99999999999999999988542 3
Q ss_pred ceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHHHHHhh
Q psy4404 68 AFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQL 118 (151)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~ 118 (151)
.|+|.+|+++|..+-.|+.|+++|.|++||.|+.|+++|+....+..||..
T Consensus 281 KFKCtECgKAFKfKHHLKEHlRIHSGEKPfeCpnCkKRFSHSGSySSHmSS 331 (1007)
T KOG3623|consen 281 KFKCTECGKAFKFKHHLKEHLRIHSGEKPFECPNCKKRFSHSGSYSSHMSS 331 (1007)
T ss_pred cccccccchhhhhHHHHHhhheeecCCCCcCCcccccccccCCcccccccc
Confidence 399999999999999999999999999999999999999999999999864
No 7
>KOG3623|consensus
Probab=99.58 E-value=3.8e-16 Score=119.24 Aligned_cols=83 Identities=24% Similarity=0.595 Sum_probs=78.2
Q ss_pred CCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHH
Q psy4404 34 DVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMK 113 (151)
Q Consensus 34 ~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~ 113 (151)
+.+..|.| +.|++.|-..++|.+|.-.|.|.+||+|.+|.++|..+-.|..|.++|.|++||.|..|+++|+....+.
T Consensus 890 te~gmyaC--DqCDK~FqKqSSLaRHKYEHsGqRPyqC~iCkKAFKHKHHLtEHkRLHSGEKPfQCdKClKRFSHSGSYS 967 (1007)
T KOG3623|consen 890 TEDGMYAC--DQCDKAFQKQSSLARHKYEHSGQRPYQCIICKKAFKHKHHLTEHKRLHSGEKPFQCDKCLKRFSHSGSYS 967 (1007)
T ss_pred CccccchH--HHHHHHHHhhHHHHHhhhhhcCCCCcccchhhHhhhhhhhhhhhhhhccCCCcchhhhhhhhcccccchH
Confidence 34557999 9999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh
Q psy4404 114 RHLQL 118 (151)
Q Consensus 114 ~H~~~ 118 (151)
+||..
T Consensus 968 QHMNH 972 (1007)
T KOG3623|consen 968 QHMNH 972 (1007)
T ss_pred hhhcc
Confidence 99863
No 8
>KOG1074|consensus
Probab=99.56 E-value=2e-15 Score=116.69 Aligned_cols=59 Identities=29% Similarity=0.524 Sum_probs=54.6
Q ss_pred eeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHHHHHhhhcCCccccc
Q psy4404 69 FHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLKHNADLSSM 127 (151)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~ 127 (151)
..|.+|++.|.+...|..|+++|++++||.|..|++.|..+..|+.||.+|...++..-
T Consensus 880 h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMgtH~w~q~~sr 938 (958)
T KOG1074|consen 880 HVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMGTHMWVQPPSR 938 (958)
T ss_pred hhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhccccccCCCcc
Confidence 57999999999999999999999999999999999999999999999999986665543
No 9
>KOG3576|consensus
Probab=99.53 E-value=2.2e-15 Score=99.56 Aligned_cols=85 Identities=25% Similarity=0.573 Sum_probs=80.0
Q ss_pred CCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHHH
Q psy4404 35 VSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKR 114 (151)
Q Consensus 35 ~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~ 114 (151)
+...|.| ..|++.|.-+.-|.+|++-|...+.+.|..||+.|...-+|.+|+++|+|.+||+|..|++.|..+-.|..
T Consensus 114 d~d~ftC--rvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsles 191 (267)
T KOG3576|consen 114 DQDSFTC--RVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLES 191 (267)
T ss_pred CCCeeee--ehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHH
Confidence 3456999 99999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcC
Q psy4404 115 HLQLKHN 121 (151)
Q Consensus 115 H~~~~~~ 121 (151)
|++..+|
T Consensus 192 hl~kvhg 198 (267)
T KOG3576|consen 192 HLKKVHG 198 (267)
T ss_pred HHHHHcC
Confidence 9987664
No 10
>KOG3608|consensus
Probab=99.39 E-value=4.8e-13 Score=95.15 Aligned_cols=109 Identities=21% Similarity=0.513 Sum_probs=79.7
Q ss_pred eeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcc--cccccCCh
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPH--CEYRCSQQ 81 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~--C~~~~~~~ 81 (151)
|+||.|+......+ +|..|+ ..+|..++||+| +.|.+.+.....|++|..+|. +..|.|.. |...+...
T Consensus 264 ykCplCdmtc~~~s-sL~~H~-----r~rHs~dkpfKC--d~Cd~~c~~esdL~kH~~~HS-~~~y~C~h~~C~~s~r~~ 334 (467)
T KOG3608|consen 264 YKCPLCDMTCSSAS-SLTTHI-----RYRHSKDKPFKC--DECDTRCVRESDLAKHVQVHS-KTVYQCEHPDCHYSVRTY 334 (467)
T ss_pred ccccccccCCCChH-HHHHHH-----HhhhccCCCccc--cchhhhhccHHHHHHHHHhcc-ccceecCCCCCcHHHHHH
Confidence 45555555555555 555555 356677888888 888888888888888888776 55688876 88888888
Q ss_pred HHHHHHHhhhC-CC--CceeCCcCCccccCHHHHHHHHhhhcC
Q psy4404 82 SALYNHLKRHT-GE--KPFKCTICSHKAARKDHMKRHLQLKHN 121 (151)
Q Consensus 82 ~~l~~h~~~h~-~~--~~~~C~~C~~~f~~~~~l~~H~~~~~~ 121 (151)
..+..|++-+. |. .+|.|-.|++.|.+-..|..|++..++
T Consensus 335 ~q~~~H~~evhEg~np~~Y~CH~Cdr~ft~G~~L~~HL~kkH~ 377 (467)
T KOG3608|consen 335 TQMRRHFLEVHEGNNPILYACHCCDRFFTSGKSLSAHLMKKHG 377 (467)
T ss_pred HHHHHHHHHhccCCCCCceeeecchhhhccchhHHHHHHHhhc
Confidence 88888876543 43 348888888888888888888776653
No 11
>PHA00733 hypothetical protein
Probab=99.18 E-value=3.8e-11 Score=75.84 Aligned_cols=87 Identities=18% Similarity=0.302 Sum_probs=70.7
Q ss_pred CCCCCCcceeeccCCCCcccCCchHHHHH--HH---hhcCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCcc
Q psy4404 31 SRPDVSFKYVCLYQKCSYHTGNSDHMRRH--IR---RHTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHK 105 (151)
Q Consensus 31 ~~~~~~~~~~C~~~~C~~~f~~~~~l~~h--~~---~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 105 (151)
......+++.| ..|.+.|.....|..+ .. .+.+.+||.|+.|++.|.....|..|++.+ +.+|.|..|++.
T Consensus 33 ~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~l~~~~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~ 108 (128)
T PHA00733 33 SLTPEQKRLIR--AVVKTLIYNPQLLDESSYLYKLLTSKAVSPYVCPLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKE 108 (128)
T ss_pred cCChhhhhHHH--HHHhhhccChhhhcchHHHHhhcccCCCCCccCCCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCc
Confidence 33445677889 8899888887777655 11 234477899999999999999999999876 457999999999
Q ss_pred ccCHHHHHHHHhhhcC
Q psy4404 106 AARKDHMKRHLQLKHN 121 (151)
Q Consensus 106 f~~~~~l~~H~~~~~~ 121 (151)
|.....|..|+...++
T Consensus 109 F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 109 FRNTDSTLDHVCKKHN 124 (128)
T ss_pred cCCHHHHHHHHHHhcC
Confidence 9999999999998775
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.17 E-value=1e-10 Score=89.35 Aligned_cols=58 Identities=17% Similarity=0.500 Sum_probs=29.5
Q ss_pred CCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccc
Q psy4404 44 QKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKA 106 (151)
Q Consensus 44 ~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 106 (151)
+.|++.|. ...|..|+..++ .++.|+ |+..+ ....|..|+.+|...+++.|..|++.+
T Consensus 457 ~~Cgk~f~-~s~LekH~~~~H--kpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v 514 (567)
T PLN03086 457 EKCGQAFQ-QGEMEKHMKVFH--EPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMV 514 (567)
T ss_pred CCCCCccc-hHHHHHHHHhcC--CCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCcc
Confidence 55555553 344555555543 345555 55433 334455555555555555555555544
No 13
>PLN03086 PRLI-interacting factor K; Provisional
Probab=99.09 E-value=3e-10 Score=86.87 Aligned_cols=102 Identities=20% Similarity=0.373 Sum_probs=81.7
Q ss_pred eeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCC--
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQ-- 80 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~-- 80 (151)
.+.|+.||+.|. .. .|..|+++|+ .++.| + ||..+ .+..|..|+..|.+.+++.|+.|+..+..
T Consensus 453 H~~C~~Cgk~f~-~s-~LekH~~~~H--------kpv~C--p-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~ 518 (567)
T PLN03086 453 HVHCEKCGQAFQ-QG-EMEKHMKVFH--------EPLQC--P-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGG 518 (567)
T ss_pred CccCCCCCCccc-hH-HHHHHHHhcC--------CCccC--C-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCc
Confidence 457999999995 45 8999976532 67899 7 99765 56899999999999999999999998852
Q ss_pred --------hHHHHHHHhhhCCCCceeCCcCCccccCHHHHHHHHhhhc
Q psy4404 81 --------QSALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLKH 120 (151)
Q Consensus 81 --------~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 120 (151)
...|..|... .+.+++.|..|++.+..+ .+..|+...|
T Consensus 519 ~~~d~~d~~s~Lt~HE~~-CG~rt~~C~~Cgk~Vrlr-dm~~H~~~~h 564 (567)
T PLN03086 519 SAMDVRDRLRGMSEHESI-CGSRTAPCDSCGRSVMLK-EMDIHQIAVH 564 (567)
T ss_pred cccchhhhhhhHHHHHHh-cCCcceEccccCCeeeeh-hHHHHHHHhh
Confidence 3478899877 488999999999988765 5667766544
No 14
>PHA00733 hypothetical protein
Probab=99.02 E-value=3.3e-10 Score=71.58 Aligned_cols=86 Identities=21% Similarity=0.306 Sum_probs=67.1
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCCh
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQ 81 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 81 (151)
+.+.|..|.+.|.+.. .|..+.-... .....+..+|.| +.|++.|.+..+|..|++.+ ..++.|..|++.|...
T Consensus 39 ~~~~~~~~~~~~~~~~-~l~~~~~l~~-~~~~~~~kPy~C--~~Cgk~Fss~s~L~~H~r~h--~~~~~C~~CgK~F~~~ 112 (128)
T PHA00733 39 KRLIRAVVKTLIYNPQ-LLDESSYLYK-LLTSKAVSPYVC--PLCLMPFSSSVSLKQHIRYT--EHSKVCPVCGKEFRNT 112 (128)
T ss_pred hhHHHHHHhhhccChh-hhcchHHHHh-hcccCCCCCccC--CCCCCcCCCHHHHHHHHhcC--CcCccCCCCCCccCCH
Confidence 4578999999998876 6666511111 223345788999 99999999999999999876 3469999999999999
Q ss_pred HHHHHHHhhhCC
Q psy4404 82 SALYNHLKRHTG 93 (151)
Q Consensus 82 ~~l~~h~~~h~~ 93 (151)
..|..|+....+
T Consensus 113 ~sL~~H~~~~h~ 124 (128)
T PHA00733 113 DSTLDHVCKKHN 124 (128)
T ss_pred HHHHHHHHHhcC
Confidence 999999875443
No 15
>PHA02768 hypothetical protein; Provisional
Probab=98.89 E-value=7.8e-10 Score=58.62 Aligned_cols=40 Identities=20% Similarity=0.434 Sum_probs=21.6
Q ss_pred eeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChH
Q psy4404 39 YVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQS 82 (151)
Q Consensus 39 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~ 82 (151)
|.| +.||+.|...++|..|++.|+ +++.|..|++.|...+
T Consensus 6 y~C--~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~~s 45 (55)
T PHA02768 6 YEC--PICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLRTG 45 (55)
T ss_pred cCc--chhCCeeccHHHHHHHHHhcC--CcccCCcccceecccc
Confidence 455 555555555555555555554 3455555555554443
No 16
>KOG3993|consensus
Probab=98.84 E-value=9.5e-10 Score=80.18 Aligned_cols=121 Identities=17% Similarity=0.225 Sum_probs=87.5
Q ss_pred eeeccccccccccCchHHHHHHhhcCCC-------------C--------------CCCCCcceeeccCCCCcccCCchH
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCKNL-------------S--------------RPDVSFKYVCLYQKCSYHTGNSDH 55 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~-------------~--------------~~~~~~~~~C~~~~C~~~f~~~~~ 55 (151)
-|+|++|+|+|.=.. +|..|.|||+-. . ....+..|.| ..|++.|.....
T Consensus 295 EYrCPEC~KVFsCPA-NLASHRRWHKPR~eaa~a~~~P~k~~~~~rae~~ea~rsg~dss~gi~~C--~~C~KkFrRqAY 371 (500)
T KOG3993|consen 295 EYRCPECDKVFSCPA-NLASHRRWHKPRPEAAKAGSPPPKQAVETRAEVQEAERSGDDSSSGIFSC--HTCGKKFRRQAY 371 (500)
T ss_pred eecCCcccccccCch-hhhhhhcccCCchhhhhcCCCChhhhhhhhhhhhhccccCCcccCceeec--HHhhhhhHHHHH
Confidence 589999999999999 999999999820 0 0012236999 999999999999
Q ss_pred HHHHHHhhcCCCc----------------------------------------------eeCcccccccCChHHHHHHHh
Q psy4404 56 MRRHIRRHTGEKA----------------------------------------------FHCPHCEYRCSQQSALYNHLK 89 (151)
Q Consensus 56 l~~h~~~h~~~~~----------------------------------------------~~C~~C~~~~~~~~~l~~h~~ 89 (151)
|+.|+.+|+.... ..++.++..+.+++.--.+.+
T Consensus 372 LrKHqlthq~~~~~k~~a~~f~~s~~~~l~~~~~~~a~h~~a~~~~g~~vl~~a~sael~~pp~~~~ppsss~~sgg~~r 451 (500)
T KOG3993|consen 372 LRKHQLTHQRAPLAKEKAPKFLLSRVIPLMHFNQAVATHSSASDSHGDEVLYVAGSAELELPPYDGSPPSSSGSSGGYGR 451 (500)
T ss_pred HHHhHHhhhccccchhcccCcchhhcccccccccccccccccccccccceeeeeccccccCCCCCCCCcccCCCCCcccc
Confidence 9999887643100 234556655555554444444
Q ss_pred hhCCCCceeCCcCCccccCHHHHHHHHhhhcCCcccc
Q psy4404 90 RHTGEKPFKCTICSHKAARKDHMKRHLQLKHNADLSS 126 (151)
Q Consensus 90 ~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~ 126 (151)
....+..|.|..|-..|.....|.+|+...|..+..+
T Consensus 452 lg~~~q~f~~ky~~atfyss~~ltrhin~~Hpse~rq 488 (500)
T KOG3993|consen 452 LGIAEQGFTCKYCPATFYSSPGLTRHINKCHPSELRQ 488 (500)
T ss_pred ccchhhccccccchHhhhcCcchHhHhhhcChHHhhh
Confidence 4444567889999999999999999998877554443
No 17
>PHA02768 hypothetical protein; Provisional
Probab=98.79 E-value=2e-09 Score=57.08 Aligned_cols=38 Identities=24% Similarity=0.621 Sum_probs=17.0
Q ss_pred eeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccC
Q psy4404 69 FHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAAR 108 (151)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~ 108 (151)
|.|+.|++.|...+.|..|+++|. ++|+|..|++.|..
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~--k~~kc~~C~k~f~~ 43 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN--TNLKLSNCKRISLR 43 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC--CcccCCcccceecc
Confidence 344444444444444444444444 24444444444443
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=98.65 E-value=2.5e-08 Score=45.30 Aligned_cols=24 Identities=46% Similarity=1.025 Sum_probs=15.0
Q ss_pred HHHHHhhhCCCCceeCCcCCcccc
Q psy4404 84 LYNHLKRHTGEKPFKCTICSHKAA 107 (151)
Q Consensus 84 l~~h~~~h~~~~~~~C~~C~~~f~ 107 (151)
|..|+++|++++||.|+.|++.|.
T Consensus 2 l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSSSEEESSSSEEES
T ss_pred HHHHhhhcCCCCCCCCCCCcCeeC
Confidence 556666666666666666666654
No 19
>KOG3993|consensus
Probab=98.57 E-value=1.8e-08 Score=73.65 Aligned_cols=108 Identities=20% Similarity=0.379 Sum_probs=73.1
Q ss_pred eeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCcee---CcccccccCC
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFH---CPHCEYRCSQ 80 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~---C~~C~~~~~~ 80 (151)
|+|..|-..|..-. .|.+| .=..+.-.-|+| ++|++.|+-..||..|++.|......- -+.=.+....
T Consensus 268 yiCqLCK~kYeD~F-~LAQH------rC~RIV~vEYrC--PEC~KVFsCPANLASHRRWHKPR~eaa~a~~~P~k~~~~~ 338 (500)
T KOG3993|consen 268 YICQLCKEKYEDAF-ALAQH------RCPRIVHVEYRC--PECDKVFSCPANLASHRRWHKPRPEAAKAGSPPPKQAVET 338 (500)
T ss_pred HHHHHHHHhhhhHH-HHhhc------cCCeeEEeeecC--CcccccccCchhhhhhhcccCCchhhhhcCCCChhhhhhh
Confidence 78999999999999 99999 223334445999 999999999999999999986542211 0000001011
Q ss_pred hHHHHHHH-hh--hCCCCceeCCcCCccccCHHHHHHHHhhhcC
Q psy4404 81 QSALYNHL-KR--HTGEKPFKCTICSHKAARKDHMKRHLQLKHN 121 (151)
Q Consensus 81 ~~~l~~h~-~~--h~~~~~~~C~~C~~~f~~~~~l~~H~~~~~~ 121 (151)
. .+.+.. +. ...+-.|.|..|++.|.+...|+.|+.+|+.
T Consensus 339 r-ae~~ea~rsg~dss~gi~~C~~C~KkFrRqAYLrKHqlthq~ 381 (500)
T KOG3993|consen 339 R-AEVQEAERSGDDSSSGIFSCHTCGKKFRRQAYLRKHQLTHQR 381 (500)
T ss_pred h-hhhhhccccCCcccCceeecHHhhhhhHHHHHHHHhHHhhhc
Confidence 1 111111 11 1223479999999999999999999988874
No 20
>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=98.55 E-value=6.4e-08 Score=43.90 Aligned_cols=25 Identities=52% Similarity=1.079 Sum_probs=18.7
Q ss_pred HHHHHHHhhcCCCceeCcccccccC
Q psy4404 55 HMRRHIRRHTGEKAFHCPHCEYRCS 79 (151)
Q Consensus 55 ~l~~h~~~h~~~~~~~C~~C~~~~~ 79 (151)
+|..|+++|++++||.|+.|++.|.
T Consensus 1 ~l~~H~~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 1 NLRRHMRTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHHHHHHHSSSSSEEESSSSEEES
T ss_pred CHHHHhhhcCCCCCCCCCCCcCeeC
Confidence 4677777777777788887777764
No 21
>PHA00616 hypothetical protein
Probab=98.41 E-value=1.4e-07 Score=47.65 Aligned_cols=32 Identities=19% Similarity=0.394 Sum_probs=21.1
Q ss_pred ceeCCcCCccccCHHHHHHHHhhhcCCccccc
Q psy4404 96 PFKCTICSHKAARKDHMKRHLQLKHNADLSSM 127 (151)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~~~~~~~~~~ 127 (151)
||+|+.||+.|...+.|..|++.|++++++.+
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred CCccchhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 46666666666666666677666666665544
No 22
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=98.23 E-value=4.5e-07 Score=39.82 Aligned_cols=21 Identities=29% Similarity=0.550 Sum_probs=12.3
Q ss_pred eeccccccccccCchHHHHHHh
Q psy4404 4 VICQYCEVRLESNSKELLEHCK 25 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~ 25 (151)
|+|+.||+.|.+.. .|..|++
T Consensus 1 y~C~~C~~~f~~~~-~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKS-NLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHH-HHHHHHH
T ss_pred CCCCCCCCccCCHH-HHHHHHh
Confidence 45666666665555 6666654
No 23
>PHA00616 hypothetical protein
Probab=98.20 E-value=6e-07 Score=45.42 Aligned_cols=28 Identities=7% Similarity=0.125 Sum_probs=13.4
Q ss_pred CCCCcccCCchHHHHHHHhhcCCCceeC
Q psy4404 44 QKCSYHTGNSDHMRRHIRRHTGEKAFHC 71 (151)
Q Consensus 44 ~~C~~~f~~~~~l~~h~~~h~~~~~~~C 71 (151)
+.||+.|.+...|..|++.|++++++.|
T Consensus 5 ~~CG~~F~~~s~l~~H~r~~hg~~~~~~ 32 (44)
T PHA00616 5 LRCGGIFRKKKEVIEHLLSVHKQNKLTL 32 (44)
T ss_pred chhhHHHhhHHHHHHHHHHhcCCCccce
Confidence 4444444444444444444444444443
No 24
>PHA00732 hypothetical protein
Probab=98.06 E-value=2.4e-06 Score=49.35 Aligned_cols=21 Identities=19% Similarity=0.392 Sum_probs=11.8
Q ss_pred eeeccccccccccCchHHHHHH
Q psy4404 3 LVICQYCEVRLESNSKELLEHC 24 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~ 24 (151)
+|+|+.||+.|.+.. .|+.|+
T Consensus 1 py~C~~Cgk~F~s~s-~Lk~H~ 21 (79)
T PHA00732 1 MFKCPICGFTTVTLF-ALKQHA 21 (79)
T ss_pred CccCCCCCCccCCHH-HHHHHh
Confidence 355555555555555 555553
No 25
>PHA00732 hypothetical protein
Probab=98.05 E-value=3.6e-06 Score=48.61 Aligned_cols=48 Identities=27% Similarity=0.561 Sum_probs=37.7
Q ss_pred ceeeccCCCCcccCCchHHHHHHHh-hcCCCceeCcccccccCChHHHHHHHhhhCC
Q psy4404 38 KYVCLYQKCSYHTGNSDHMRRHIRR-HTGEKAFHCPHCEYRCSQQSALYNHLKRHTG 93 (151)
Q Consensus 38 ~~~C~~~~C~~~f~~~~~l~~h~~~-h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~ 93 (151)
||.| +.|++.|.+..+|..|++. |.+ +.|+.|++.|.. +..|.++..+
T Consensus 1 py~C--~~Cgk~F~s~s~Lk~H~r~~H~~---~~C~~CgKsF~~---l~~H~~~~~~ 49 (79)
T PHA00732 1 MFKC--PICGFTTVTLFALKQHARRNHTL---TKCPVCNKSYRR---LNQHFYSQYD 49 (79)
T ss_pred CccC--CCCCCccCCHHHHHHHhhcccCC---CccCCCCCEeCC---hhhhhcccCC
Confidence 4778 8999999999999999874 543 579999999874 6677765554
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=98.04 E-value=3.6e-06 Score=45.11 Aligned_cols=51 Identities=33% Similarity=0.663 Sum_probs=31.0
Q ss_pred eeeccccccccccCchHHHHHHhhcCCCCCCCC-CcceeeccCCCCcccCCchHHHHHHHhhc
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCKNLSRPDV-SFKYVCLYQKCSYHTGNSDHMRRHIRRHT 64 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~-~~~~~C~~~~C~~~f~~~~~l~~h~~~h~ 64 (151)
.|.||.||+.| +.. .|..|+.. .|.. .+.+.| +.|...+. .+|..|+..++
T Consensus 2 ~f~CP~C~~~~-~~~-~L~~H~~~-----~H~~~~~~v~C--PiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 2 SFTCPYCGKGF-SES-SLVEHCED-----EHRSESKNVVC--PICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred CcCCCCCCCcc-CHH-HHHHHHHh-----HCcCCCCCccC--CCchhhhh--hHHHHHHHHhc
Confidence 47788888844 445 78877643 2332 235777 77876544 36777766543
No 27
>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=98.00 E-value=2.9e-06 Score=37.32 Aligned_cols=22 Identities=36% Similarity=0.646 Sum_probs=12.7
Q ss_pred eeccccccccccCchHHHHHHhh
Q psy4404 4 VICQYCEVRLESNSKELLEHCKT 26 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~ 26 (151)
|+|+.|++.|.+.. .|..|+++
T Consensus 1 ~~C~~C~~~~~~~~-~l~~H~~~ 22 (24)
T PF13894_consen 1 FQCPICGKSFRSKS-ELRQHMRT 22 (24)
T ss_dssp EE-SSTS-EESSHH-HHHHHHHH
T ss_pred CCCcCCCCcCCcHH-HHHHHHHh
Confidence 56666666666666 66666544
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=97.94 E-value=4.2e-06 Score=38.16 Aligned_cols=23 Identities=30% Similarity=0.436 Sum_probs=15.6
Q ss_pred eeeccccccccccCchHHHHHHhh
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKT 26 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~ 26 (151)
||.|..|++.|.+.. .|..|++.
T Consensus 1 ~~~C~~C~~~F~~~~-~l~~H~~~ 23 (27)
T PF13912_consen 1 PFECDECGKTFSSLS-ALREHKRS 23 (27)
T ss_dssp SEEETTTTEEESSHH-HHHHHHCT
T ss_pred CCCCCccCCccCChh-HHHHHhHH
Confidence 467777777777777 77777543
No 29
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.87 E-value=2.5e-06 Score=60.69 Aligned_cols=72 Identities=19% Similarity=0.432 Sum_probs=48.7
Q ss_pred CcceeeccCCCCcccCCchHHHHHHHh-hcCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHHH
Q psy4404 36 SFKYVCLYQKCSYHTGNSDHMRRHIRR-HTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKR 114 (151)
Q Consensus 36 ~~~~~C~~~~C~~~f~~~~~l~~h~~~-h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~ 114 (151)
++||+|+.+.|.+.+..+..|+-|+.- |...+...-+. -..+...-...+||+|++|++++.....|..
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~----------p~~~~~F~~~~KPYrCevC~KRYKNlNGLKY 416 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPS----------PEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCC----------ccccccccccCCceeccccchhhccCcccee
Confidence 489999999999999999999999753 32222111110 0011111234689999999999999888888
Q ss_pred HHh
Q psy4404 115 HLQ 117 (151)
Q Consensus 115 H~~ 117 (151)
|+.
T Consensus 417 Hr~ 419 (423)
T COG5189 417 HRK 419 (423)
T ss_pred ccc
Confidence 864
No 30
>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=97.80 E-value=2.2e-05 Score=34.25 Aligned_cols=23 Identities=35% Similarity=0.868 Sum_probs=16.7
Q ss_pred eeeccCCCCcccCCchHHHHHHHhh
Q psy4404 39 YVCLYQKCSYHTGNSDHMRRHIRRH 63 (151)
Q Consensus 39 ~~C~~~~C~~~f~~~~~l~~h~~~h 63 (151)
|.| +.|++.|.+...|..|++.|
T Consensus 1 y~C--~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKC--PICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEE--TTTTEEESSHHHHHHHHHHH
T ss_pred CCC--CCCCCccCCHHHHHHHHhHC
Confidence 567 77777777777777777653
No 31
>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=97.80 E-value=5.5e-05 Score=40.48 Aligned_cols=49 Identities=39% Similarity=0.763 Sum_probs=22.9
Q ss_pred eeCcccccccCChHHHHHHHhh-hCCC-CceeCCcCCccccCHHHHHHHHhhhc
Q psy4404 69 FHCPHCEYRCSQQSALYNHLKR-HTGE-KPFKCTICSHKAARKDHMKRHLQLKH 120 (151)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~h~~~-h~~~-~~~~C~~C~~~f~~~~~l~~H~~~~~ 120 (151)
|.||.|++ ..+...|..|... |..+ +.+.|++|...+. .+|..|+...+
T Consensus 3 f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~~~--~~l~~Hl~~~H 53 (54)
T PF05605_consen 3 FTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSRVT--DNLIRHLNSQH 53 (54)
T ss_pred cCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhhhh--hHHHHHHHHhc
Confidence 45555555 3334445555432 3322 2355555554322 35555655443
No 32
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=97.71 E-value=3.1e-05 Score=35.18 Aligned_cols=25 Identities=20% Similarity=0.559 Sum_probs=19.4
Q ss_pred ceeCCcCCccccCHHHHHHHHhhhc
Q psy4404 96 PFKCTICSHKAARKDHMKRHLQLKH 120 (151)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~~~ 120 (151)
||.|..|++.|.....|..|++.|.
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h~ 25 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSHC 25 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTTT
T ss_pred CCCCCccCCccCChhHHHHHhHHhc
Confidence 5778888888888888888877665
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=97.68 E-value=5.2e-05 Score=33.12 Aligned_cols=24 Identities=29% Similarity=0.837 Sum_probs=15.8
Q ss_pred eeCCcCCccccCHHHHHHHHhhhc
Q psy4404 97 FKCTICSHKAARKDHMKRHLQLKH 120 (151)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~~ 120 (151)
|.|+.|++.|.....|..|++.++
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 567777777777777777777653
No 34
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=97.60 E-value=2.7e-05 Score=55.53 Aligned_cols=22 Identities=18% Similarity=0.353 Sum_probs=20.8
Q ss_pred ceeeccc--cccccccCchHHHHHH
Q psy4404 2 ILVICQY--CEVRLESNSKELLEHC 24 (151)
Q Consensus 2 ~~~~C~~--C~~~f~~~~~~l~~H~ 24 (151)
+||+||+ |+|.+++.. .|..|+
T Consensus 348 KpykCpV~gC~K~Yknqn-GLKYH~ 371 (423)
T COG5189 348 KPYKCPVEGCNKKYKNQN-GLKYHM 371 (423)
T ss_pred ceecCCCCCchhhhcccc-chhhhh
Confidence 7999999 999999999 999995
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.47 E-value=8.9e-05 Score=44.49 Aligned_cols=74 Identities=23% Similarity=0.541 Sum_probs=20.2
Q ss_pred eccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHH
Q psy4404 5 ICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSAL 84 (151)
Q Consensus 5 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l 84 (151)
.|..|+..|.+.. .|..||...++...... ..+.....+....+.-. ...+.|..|+..|.+...|
T Consensus 1 ~C~~C~~~f~~~~-~l~~H~~~~H~~~~~~~------------~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l 66 (100)
T PF12756_consen 1 QCLFCDESFSSVD-DLLQHMKKKHGFDIPDQ------------KYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREAL 66 (100)
T ss_dssp --------------------------------------------------------------SSEEBSSSS-EESSHHHH
T ss_pred Ccccccccccccc-ccccccccccccccccc------------ccccccccccccccccc-CCCCCCCccCCCCcCHHHH
Confidence 4899999999998 99999754443322211 11112222323322221 2258899999999988889
Q ss_pred HHHHhhhC
Q psy4404 85 YNHLKRHT 92 (151)
Q Consensus 85 ~~h~~~h~ 92 (151)
..|++.+.
T Consensus 67 ~~Hm~~~~ 74 (100)
T PF12756_consen 67 QEHMRSKH 74 (100)
T ss_dssp HHHHHHTT
T ss_pred HHHHcCcc
Confidence 99987654
No 36
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=97.33 E-value=0.00025 Score=42.50 Aligned_cols=74 Identities=20% Similarity=0.524 Sum_probs=22.5
Q ss_pred eeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHHHHHhhh
Q psy4404 40 VCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 40 ~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
.| ..|+..|.+...|..|+...++-.. +. ...+.....+..+..... ...+.|..|+..|.....|..|++.+
T Consensus 1 ~C--~~C~~~f~~~~~l~~H~~~~H~~~~---~~-~~~l~~~~~~~~~~~~~~-~~~~~C~~C~~~f~s~~~l~~Hm~~~ 73 (100)
T PF12756_consen 1 QC--LFCDESFSSVDDLLQHMKKKHGFDI---PD-QKYLVDPNRLLNYLRKKV-KESFRCPYCNKTFRSREALQEHMRSK 73 (100)
T ss_dssp -------------------------------------------------------SSEEBSSSS-EESSHHHHHHHHHHT
T ss_pred Cc--ccccccccccccccccccccccccc---cc-cccccccccccccccccc-CCCCCCCccCCCCcCHHHHHHHHcCc
Confidence 37 7899999999999999876554321 11 111222233333332211 23689999999999999999999976
Q ss_pred c
Q psy4404 120 H 120 (151)
Q Consensus 120 ~ 120 (151)
.
T Consensus 74 ~ 74 (100)
T PF12756_consen 74 H 74 (100)
T ss_dssp T
T ss_pred c
Confidence 4
No 37
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=97.21 E-value=0.00018 Score=32.06 Aligned_cols=23 Identities=35% Similarity=0.713 Sum_probs=17.5
Q ss_pred eeeccccccccccCchHHHHHHhhc
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTC 27 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~ 27 (151)
+.+|+.||+.| ... .|..|+..|
T Consensus 2 l~~C~~CgR~F-~~~-~l~~H~~~C 24 (25)
T PF13913_consen 2 LVPCPICGRKF-NPD-RLEKHEKIC 24 (25)
T ss_pred CCcCCCCCCEE-CHH-HHHHHHHhc
Confidence 46799999999 444 899996554
No 38
>smart00355 ZnF_C2H2 zinc finger.
Probab=97.18 E-value=0.00016 Score=31.96 Aligned_cols=20 Identities=35% Similarity=0.582 Sum_probs=10.7
Q ss_pred eccccccccccCchHHHHHHh
Q psy4404 5 ICQYCEVRLESNSKELLEHCK 25 (151)
Q Consensus 5 ~C~~C~~~f~~~~~~l~~H~~ 25 (151)
.|+.|++.|.... .|..|++
T Consensus 2 ~C~~C~~~f~~~~-~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKS-ALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHH-HHHHHHH
Confidence 4555555555555 5555543
No 39
>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=96.99 E-value=0.00017 Score=32.77 Aligned_cols=21 Identities=29% Similarity=0.637 Sum_probs=16.1
Q ss_pred eeccccccccccCchHHHHHHh
Q psy4404 4 VICQYCEVRLESNSKELLEHCK 25 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~ 25 (151)
|.|..|++.|.+.. .+..|++
T Consensus 2 ~~C~~C~k~f~~~~-~~~~H~~ 22 (27)
T PF12171_consen 2 FYCDACDKYFSSEN-QLKQHMK 22 (27)
T ss_dssp CBBTTTTBBBSSHH-HHHCCTT
T ss_pred CCcccCCCCcCCHH-HHHHHHc
Confidence 67888888888877 8888743
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=96.92 E-value=0.0011 Score=29.14 Aligned_cols=23 Identities=22% Similarity=0.631 Sum_probs=15.4
Q ss_pred eeCCcCCccccCHHHHHHHHhhh
Q psy4404 97 FKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
|.|..|++.|.....|..|++.|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 45666777777777777776644
No 41
>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=96.83 E-value=0.00094 Score=34.69 Aligned_cols=30 Identities=23% Similarity=0.361 Sum_probs=12.3
Q ss_pred CcceeeccCCCCcccCCchHHHHHHHhhcCCC
Q psy4404 36 SFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEK 67 (151)
Q Consensus 36 ~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~ 67 (151)
+.|-.| +.|+..+.+..+|.+|+..+++.+
T Consensus 22 ~~PatC--P~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 22 EQPATC--PICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp S--EE---TTT--EESSHHHHHHHHHHHTTTS
T ss_pred CCCCCC--CcchhhccchhhHHHHHHHHhccc
Confidence 344445 555555555555555554444433
No 42
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=96.82 E-value=0.0017 Score=28.44 Aligned_cols=24 Identities=42% Similarity=0.855 Sum_probs=17.0
Q ss_pred eeCCcCCccccCHHHHHHHHhhhcC
Q psy4404 97 FKCTICSHKAARKDHMKRHLQLKHN 121 (151)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~~~ 121 (151)
|.|+.|+.... ...|..|++.+++
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 67888887777 7788888887653
No 43
>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=96.73 E-value=0.0042 Score=32.31 Aligned_cols=34 Identities=29% Similarity=0.451 Sum_probs=23.9
Q ss_pred hcCCCceeCcccccccCChHHHHHHHhhhCCCCc
Q psy4404 63 HTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKP 96 (151)
Q Consensus 63 h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~ 96 (151)
+..+.|..|++|+..+....+|..|+....+.+|
T Consensus 19 ~~S~~PatCP~C~a~~~~srnLrRHle~~H~~k~ 52 (54)
T PF09237_consen 19 SQSEQPATCPICGAVIRQSRNLRRHLEIRHFKKP 52 (54)
T ss_dssp CTTS--EE-TTT--EESSHHHHHHHHHHHTTTS-
T ss_pred hccCCCCCCCcchhhccchhhHHHHHHHHhcccC
Confidence 3456788999999999999999999988877765
No 44
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.72 E-value=0.0015 Score=28.79 Aligned_cols=23 Identities=30% Similarity=0.795 Sum_probs=17.2
Q ss_pred eeCCcCCccccCHHHHHHHHhhh
Q psy4404 97 FKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
|.|..|+..|.....+..|++.+
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 56777888888888888877654
No 45
>PRK04860 hypothetical protein; Provisional
Probab=96.32 E-value=0.0042 Score=40.84 Aligned_cols=36 Identities=22% Similarity=0.626 Sum_probs=19.3
Q ss_pred ceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCcccc
Q psy4404 68 AFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAA 107 (151)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~ 107 (151)
+|.|. |+. ....+..|.+++.++++|.|..|+..|.
T Consensus 119 ~Y~C~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 119 PYRCK-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEcC-CCC---eeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 35555 554 3334555555566555566666655443
No 46
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=96.14 E-value=0.0041 Score=30.43 Aligned_cols=36 Identities=22% Similarity=0.471 Sum_probs=25.7
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccC
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTG 51 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~ 51 (151)
|...||.|+..|.-.. .....+....+| +.|+..|.
T Consensus 1 M~i~CP~C~~~f~v~~------------~~l~~~~~~vrC--~~C~~~f~ 36 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPD------------DKLPAGGRKVRC--PKCGHVFR 36 (37)
T ss_pred CEEECCCCCceEEcCH------------HHcccCCcEEEC--CCCCcEee
Confidence 5678999999987665 223345557888 88988774
No 47
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.12 E-value=0.0053 Score=27.00 Aligned_cols=19 Identities=26% Similarity=0.658 Sum_probs=9.2
Q ss_pred eeccccccccccCchHHHHH
Q psy4404 4 VICQYCEVRLESNSKELLEH 23 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H 23 (151)
|.|..|++.|.+.. .|+.|
T Consensus 1 ~~C~~C~~~f~s~~-~~~~H 19 (25)
T PF12874_consen 1 FYCDICNKSFSSEN-SLRQH 19 (25)
T ss_dssp EEETTTTEEESSHH-HHHHH
T ss_pred CCCCCCCCCcCCHH-HHHHH
Confidence 34445555554444 44444
No 48
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.93 E-value=0.0076 Score=29.27 Aligned_cols=36 Identities=22% Similarity=0.471 Sum_probs=25.6
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccC
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTG 51 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~ 51 (151)
|.+.|+.|+..|.-.. ..........+| +.|+..|.
T Consensus 1 M~i~Cp~C~~~y~i~d------------~~ip~~g~~v~C--~~C~~~f~ 36 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDD------------EKIPPKGRKVRC--SKCGHVFF 36 (36)
T ss_pred CEEECCCCCCEEeCCH------------HHCCCCCcEEEC--CCCCCEeC
Confidence 5678999999986655 233455566888 88888763
No 49
>PRK04860 hypothetical protein; Provisional
Probab=95.84 E-value=0.01 Score=39.06 Aligned_cols=39 Identities=31% Similarity=0.658 Sum_probs=33.1
Q ss_pred cceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCCh
Q psy4404 37 FKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQ 81 (151)
Q Consensus 37 ~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 81 (151)
-+|.| . |+. ....+..|.++|.++++|.|..|+..|...
T Consensus 118 ~~Y~C--~-C~~---~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 118 FPYRC--K-CQE---HQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEEc--C-CCC---eeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 35889 7 887 667889999999999999999999887543
No 50
>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=95.80 E-value=0.0069 Score=29.70 Aligned_cols=36 Identities=19% Similarity=0.291 Sum_probs=23.9
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccC
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTG 51 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~ 51 (151)
|.+.||.|+..|.-.. +.. ........| +.|+..|.
T Consensus 1 M~~~CP~C~~~~~v~~-~~~-----------~~~~~~v~C--~~C~~~~~ 36 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVD-SQL-----------GANGGKVRC--GKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEEEeCH-HHc-----------CCCCCEEEC--CCCCCEEE
Confidence 5678999999987765 221 122235778 88988764
No 51
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=95.46 E-value=0.0057 Score=27.56 Aligned_cols=22 Identities=14% Similarity=0.673 Sum_probs=16.2
Q ss_pred eeeccCCCCcccCCchHHHHHHHh
Q psy4404 39 YVCLYQKCSYHTGNSDHMRRHIRR 62 (151)
Q Consensus 39 ~~C~~~~C~~~f~~~~~l~~h~~~ 62 (151)
|.| ..|++.|.+...+..|+++
T Consensus 2 ~~C--~~C~k~f~~~~~~~~H~~s 23 (27)
T PF12171_consen 2 FYC--DACDKYFSSENQLKQHMKS 23 (27)
T ss_dssp CBB--TTTTBBBSSHHHHHCCTTS
T ss_pred CCc--ccCCCCcCCHHHHHHHHcc
Confidence 567 7788888887777777654
No 52
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=95.33 E-value=0.021 Score=24.79 Aligned_cols=19 Identities=42% Similarity=1.031 Sum_probs=8.8
Q ss_pred CCCCcccCCchHHHHHHHhh
Q psy4404 44 QKCSYHTGNSDHMRRHIRRH 63 (151)
Q Consensus 44 ~~C~~~f~~~~~l~~h~~~h 63 (151)
+.|..... ...|..|++.+
T Consensus 4 ~~C~y~t~-~~~l~~H~~~~ 22 (24)
T PF13909_consen 4 PHCSYSTS-KSNLKRHLKRH 22 (24)
T ss_dssp SSSS-EES-HHHHHHHHHHH
T ss_pred CCCCCcCC-HHHHHHHHHhh
Confidence 44555444 44555554443
No 53
>KOG2231|consensus
Probab=95.22 E-value=0.034 Score=44.32 Aligned_cols=67 Identities=19% Similarity=0.361 Sum_probs=38.3
Q ss_pred cCCchHHHHHHHhhcC-CC----ceeCcccccccCChHHHHHHHhhhCCCCceeCCcCC------ccccCHHHHHHHHhh
Q psy4404 50 TGNSDHMRRHIRRHTG-EK----AFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICS------HKAARKDHMKRHLQL 118 (151)
Q Consensus 50 f~~~~~l~~h~~~h~~-~~----~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~------~~f~~~~~l~~H~~~ 118 (151)
..+...|..|+..-.. .. --.|..|...|.....+..|++.+. |.|..|. ..|.....|..|.+.
T Consensus 159 ~Yt~~el~~h~~~gd~d~~s~rGhp~C~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR~ 234 (669)
T KOG2231|consen 159 LYTRAELNLHLMFGDPDDESCRGHPLCKFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFRK 234 (669)
T ss_pred hehHHHHHHHHhcCCCccccccCCccchhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhhh
Confidence 4444666666554222 11 1357777777777777777766433 3444442 355566667777666
Q ss_pred hc
Q psy4404 119 KH 120 (151)
Q Consensus 119 ~~ 120 (151)
.|
T Consensus 235 ~H 236 (669)
T KOG2231|consen 235 GH 236 (669)
T ss_pred cC
Confidence 55
No 54
>KOG1146|consensus
Probab=94.79 E-value=0.0084 Score=50.60 Aligned_cols=58 Identities=17% Similarity=0.327 Sum_probs=45.2
Q ss_pred ceeeccccccccccCchHHHHHHhhcCC-------------------CCCCCCCcceeeccCCCCcccCCchHHHHHHHh
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKN-------------------LSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRR 62 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~-------------------~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~ 62 (151)
+.|+|+.|+..|+... .|..|||.-+. ..---+.++|.| ..|...+....+|..|+..
T Consensus 464 kt~~cpkc~~~yk~a~-~L~vhmRskhp~~~~~~c~~gq~~~~~arg~~~~~~~~p~~C--~~C~~stttng~LsihlqS 540 (1406)
T KOG1146|consen 464 KTLKCPKCNWHYKLAQ-TLGVHMRSKHPESQSAYCKAGQNHPRLARGEVYRCPGKPYPC--RACNYSTTTNGNLSIHLQS 540 (1406)
T ss_pred ccccCCccchhhhhHH-HhhhcccccccccchhHhHhccccccccccccccCCCCcccc--eeeeeeeecchHHHHHHHH
Confidence 4589999999999999 99999887331 111123457888 8899999999999999865
No 55
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.79 E-value=0.037 Score=28.35 Aligned_cols=32 Identities=22% Similarity=0.444 Sum_probs=22.4
Q ss_pred CceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccC
Q psy4404 1 MILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTG 51 (151)
Q Consensus 1 ~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~ 51 (151)
|+.|+|+.||..|.... .. . ...| +.||..+.
T Consensus 1 ~~~y~C~~CG~~~~~~~------------~~---~--~~~C--p~CG~~~~ 32 (46)
T PRK00398 1 MAEYKCARCGREVELDE------------YG---T--GVRC--PYCGYRIL 32 (46)
T ss_pred CCEEECCCCCCEEEECC------------CC---C--ceEC--CCCCCeEE
Confidence 67899999999886655 11 1 4678 77886543
No 56
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=94.12 E-value=0.028 Score=26.75 Aligned_cols=21 Identities=19% Similarity=0.458 Sum_probs=13.7
Q ss_pred eeeccccccccccCchHHHHHH
Q psy4404 3 LVICQYCEVRLESNSKELLEHC 24 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~ 24 (151)
.|.|..|++.|.+.. .+..|+
T Consensus 3 ~~~C~~C~~~~~~~~-~~~~H~ 23 (35)
T smart00451 3 GFYCKLCNVTFTDEI-SVEAHL 23 (35)
T ss_pred CeEccccCCccCCHH-HHHHHH
Confidence 456777777776555 666664
No 57
>KOG1146|consensus
Probab=93.87 E-value=0.017 Score=48.93 Aligned_cols=103 Identities=20% Similarity=0.303 Sum_probs=63.3
Q ss_pred ccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHH
Q psy4404 6 CQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALY 85 (151)
Q Consensus 6 C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~ 85 (151)
|..|+..|.+.. .+..|+ ...+.-.+-|.| +.|+..|+....|-.||++.+.+... ..|..+- .-..+.
T Consensus 439 ~~~~e~~~~s~r-~~~~~t-----~~L~S~~kt~~c--pkc~~~yk~a~~L~vhmRskhp~~~~--~~c~~gq-~~~~~a 507 (1406)
T KOG1146|consen 439 LTKAEPLLESKR-SLEGQT-----VVLHSFFKTLKC--PKCNWHYKLAQTLGVHMRSKHPESQS--AYCKAGQ-NHPRLA 507 (1406)
T ss_pred ccchhhhhhhhc-ccccce-----eeeecccccccC--CccchhhhhHHHhhhcccccccccch--hHhHhcc-cccccc
Confidence 455566666655 666664 234444577889 88999999999999998874433211 2222111 101111
Q ss_pred HHHhhhCCCCceeCCcCCccccCHHHHHHHHhhh
Q psy4404 86 NHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 86 ~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
.-...-.+.++|.|..|...+.....|.+|++.-
T Consensus 508 rg~~~~~~~~p~~C~~C~~stttng~LsihlqS~ 541 (1406)
T KOG1146|consen 508 RGEVYRCPGKPYPCRACNYSTTTNGNLSIHLQSD 541 (1406)
T ss_pred ccccccCCCCcccceeeeeeeecchHHHHHHHHH
Confidence 1111123456899999999999999999998853
No 58
>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=93.52 E-value=0.092 Score=24.87 Aligned_cols=24 Identities=25% Similarity=0.499 Sum_probs=19.0
Q ss_pred ceeCCcCCccccCHHHHHHHHhhh
Q psy4404 96 PFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
+|.|..|+..|.....+..|++..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk 26 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGK 26 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChH
Confidence 577888888888888888887653
No 59
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=93.42 E-value=0.033 Score=29.49 Aligned_cols=23 Identities=13% Similarity=0.491 Sum_probs=17.6
Q ss_pred ceeeccccccccccCchHHHHHHh
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCK 25 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~ 25 (151)
..+.||.||..|+... ++..|+.
T Consensus 16 ~~lrCPRC~~~FR~~K-~Y~RHVN 38 (65)
T COG4049 16 EFLRCPRCGMVFRRRK-DYIRHVN 38 (65)
T ss_pred eeeeCCchhHHHHHhH-HHHHHhh
Confidence 3577888888888777 8888853
No 60
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=92.98 E-value=0.045 Score=40.99 Aligned_cols=62 Identities=23% Similarity=0.389 Sum_probs=49.9
Q ss_pred eeeccccccccccCchHHHHHHhhcCCCC--CCCCC--cceeeccCCCCcccCCchHHHHHHHhhcCCCceeC
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCKNLS--RPDVS--FKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHC 71 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~--~~~~~--~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C 71 (151)
++.|..|...|.... .|..| .. .|+++ +++.|++..|++.|.....+..|...|....+..+
T Consensus 289 ~~~~~~~~~~~s~~~-~l~~~------~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSS-PLTRH------LRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccc-ccccc------ccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 577889999999888 99999 55 68888 89999433799999999999999888876554433
No 61
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.56 E-value=0.22 Score=30.68 Aligned_cols=24 Identities=17% Similarity=0.376 Sum_probs=12.8
Q ss_pred ceeCCcCCccccCHHHHHHHHhhh
Q psy4404 96 PFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
.|.|+.|...|-..-+.-.|...|
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe~Lh 104 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHESLH 104 (112)
T ss_pred ceeCCCCCCccccccchhhhhhcc
Confidence 455655555555555555554444
No 62
>KOG2785|consensus
Probab=92.09 E-value=0.39 Score=35.74 Aligned_cols=51 Identities=16% Similarity=0.436 Sum_probs=40.4
Q ss_pred ceeCcccccccCChHHHHHHHhhhCC-----------------------CCceeCCcCC---ccccCHHHHHHHHhh
Q psy4404 68 AFHCPHCEYRCSQQSALYNHLKRHTG-----------------------EKPFKCTICS---HKAARKDHMKRHLQL 118 (151)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~h~~~h~~-----------------------~~~~~C~~C~---~~f~~~~~l~~H~~~ 118 (151)
|-.|..|+..+.....-..||..++| ..-+.|..|+ +.|.+....+.||..
T Consensus 166 Pt~CLfC~~~~k~~e~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~CL~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLEENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFICLFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHHHHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceEEEeccccCcccccHHHHHHHhh
Confidence 35688898888888888888876654 2346788888 899999999999874
No 63
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.60 E-value=0.11 Score=28.01 Aligned_cols=33 Identities=18% Similarity=0.505 Sum_probs=18.7
Q ss_pred cceeeccCCCCcccCCchHHHHHHHhhcCCCceeCccccc
Q psy4404 37 FKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEY 76 (151)
Q Consensus 37 ~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~ 76 (151)
..|.| +.||..--.+..- --.-..+|.|+.||.
T Consensus 26 v~F~C--PnCGe~~I~Rc~~-----CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 26 VKFPC--PNCGEVEIYRCAK-----CRKLGNPYRCPKCGF 58 (61)
T ss_pred eEeeC--CCCCceeeehhhh-----HHHcCCceECCCcCc
Confidence 45778 7788554444421 111235688888864
No 64
>KOG2186|consensus
Probab=90.79 E-value=0.27 Score=34.56 Aligned_cols=49 Identities=18% Similarity=0.545 Sum_probs=36.5
Q ss_pred CceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHH
Q psy4404 1 MILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIR 61 (151)
Q Consensus 1 ~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~ 61 (151)
|.-|.|..||....-. .+..|+..|.+ .-|.| -+|++.|.. .+...|..
T Consensus 1 MV~FtCnvCgEsvKKp--~vekH~srCrn-------~~fSC--IDC~k~F~~-~sYknH~k 49 (276)
T KOG2186|consen 1 MVFFTCNVCGESVKKP--QVEKHMSRCRN-------AYFSC--IDCGKTFER-VSYKNHTK 49 (276)
T ss_pred CeEEehhhhhhhcccc--chHHHHHhccC-------CeeEE--eeccccccc-chhhhhhh
Confidence 5678899999998663 68889654433 45889 999999999 44556644
No 65
>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=90.79 E-value=0.18 Score=23.81 Aligned_cols=8 Identities=38% Similarity=1.501 Sum_probs=4.2
Q ss_pred ceeCCcCC
Q psy4404 96 PFKCTICS 103 (151)
Q Consensus 96 ~~~C~~C~ 103 (151)
++.|+.|+
T Consensus 17 ~~~CP~Cg 24 (33)
T cd00350 17 PWVCPVCG 24 (33)
T ss_pred CCcCcCCC
Confidence 44555554
No 66
>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=90.65 E-value=1.2 Score=27.24 Aligned_cols=23 Identities=26% Similarity=0.641 Sum_probs=18.5
Q ss_pred ceeeccccccccccCchHHHHHHhh
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKT 26 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~ 26 (151)
++.+|..|+-.... + ++..|++.
T Consensus 10 ~vlIC~~C~~av~~-~-~v~~HL~~ 32 (109)
T PF12013_consen 10 RVLICRQCQYAVQP-S-EVESHLRK 32 (109)
T ss_pred CEEEeCCCCcccCc-h-HHHHHHHH
Confidence 57889999988766 5 89999774
No 67
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.02 E-value=0.12 Score=35.83 Aligned_cols=49 Identities=12% Similarity=0.310 Sum_probs=27.8
Q ss_pred ceeeccccccccccCchHHHHHHhh---cCCCCCC-CCCcc-----eeeccCCCCcccCCc
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKT---CKNLSRP-DVSFK-----YVCLYQKCSYHTGNS 53 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~---~~~~~~~-~~~~~-----~~C~~~~C~~~f~~~ 53 (151)
+-+.||.|++.|.++. -+....+. ..+...+ .+..| ..| +.||..+...
T Consensus 4 k~~~CPvC~~~F~~~~-vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vC--P~CgyA~~~~ 61 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKK-VRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVC--PHCGYAAFEE 61 (214)
T ss_pred CceECCCCCCeeeeeE-EEcCCceEeeecCCCccccCCCCCeeeeEEEC--CCCCCccccc
Confidence 5688999999999876 33333111 1111122 12233 347 8888876654
No 68
>COG5048 FOG: Zn-finger [General function prediction only]
Probab=89.82 E-value=0.093 Score=39.30 Aligned_cols=60 Identities=33% Similarity=0.686 Sum_probs=40.8
Q ss_pred ceeCcccccccCChHHHHHHHh--hhCCC--CceeCC--cCCccccCHHHHHHHHhhhcCCccccc
Q psy4404 68 AFHCPHCEYRCSQQSALYNHLK--RHTGE--KPFKCT--ICSHKAARKDHMKRHLQLKHNADLSSM 127 (151)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~h~~--~h~~~--~~~~C~--~C~~~f~~~~~l~~H~~~~~~~~~~~~ 127 (151)
++.|..|...|.....+..|.+ .|.++ +|+.|+ .|++.|.+...+..|..+|.+..+..+
T Consensus 289 ~~~~~~~~~~~s~~~~l~~~~~~~~h~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 354 (467)
T COG5048 289 PIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKE 354 (467)
T ss_pred CCCCccccCCccccccccccccccccccccCCceeeeccCCCccccccccccCCcccccCCCcccc
Confidence 4566667777777777777776 67777 677777 577777777777777777665554444
No 69
>KOG4173|consensus
Probab=89.39 E-value=0.14 Score=34.87 Aligned_cols=80 Identities=20% Similarity=0.456 Sum_probs=60.2
Q ss_pred ceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHHHHHhhhC----------CCCceeCCc--CCcc
Q psy4404 38 KYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHT----------GEKPFKCTI--CSHK 105 (151)
Q Consensus 38 ~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~----------~~~~~~C~~--C~~~ 105 (151)
.+.|+.-.|...|...+....|...-++. .|.+|.+.|++.-.|-.|..-.. |.-.|.|.+ |+..
T Consensus 79 ~~~cqvagc~~~~d~lD~~E~hY~~~h~~---sCs~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~ClvEgCt~K 155 (253)
T KOG4173|consen 79 AFACQVAGCCQVFDALDDYEHHYHTLHGN---SCSFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQCLVEGCTEK 155 (253)
T ss_pred cccccccchHHHHhhhhhHHHhhhhcccc---hhHHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHHHHHhhhhh
Confidence 36787778999999988888887665442 69999999999888877764322 333488855 9999
Q ss_pred ccCHHHHHHHHhhhc
Q psy4404 106 AARKDHMKRHLQLKH 120 (151)
Q Consensus 106 f~~~~~l~~H~~~~~ 120 (151)
|.+......|+-..+
T Consensus 156 FkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 156 FKTSRDRKDHMIRMH 170 (253)
T ss_pred hhhhhhhhhHHHHhc
Confidence 999888888876543
No 70
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=89.02 E-value=0.35 Score=31.35 Aligned_cols=41 Identities=17% Similarity=0.400 Sum_probs=24.9
Q ss_pred CCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCC
Q psy4404 34 DVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQ 80 (151)
Q Consensus 34 ~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 80 (151)
.....|.| +.|+..|..-..+..- .. ...|.|+.|+.....
T Consensus 95 ~~~~~Y~C--p~C~~~y~~~ea~~~~---d~-~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 95 TNNAYYKC--PNCQSKYTFLEANQLL---DM-DGTFTCPRCGEELEE 135 (147)
T ss_pred cCCcEEEC--cCCCCEeeHHHHHHhc---CC-CCcEECCCCCCEEEE
Confidence 34556888 7788887765544321 11 234888888876643
No 71
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=88.87 E-value=0.43 Score=29.28 Aligned_cols=30 Identities=17% Similarity=0.503 Sum_probs=20.6
Q ss_pred eeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCCh
Q psy4404 39 YVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQ 81 (151)
Q Consensus 39 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~ 81 (151)
..| +.||+.|..- ++.|..||.||..|...
T Consensus 10 R~C--p~CG~kFYDL-----------nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 10 RTC--PSCGAKFYDL-----------NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred ccC--CCCcchhccC-----------CCCCccCCCCCCccCcc
Confidence 457 7788887773 24567788888777655
No 72
>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=88.53 E-value=0.33 Score=24.31 Aligned_cols=14 Identities=21% Similarity=0.427 Sum_probs=8.6
Q ss_pred eeccccccccccCc
Q psy4404 4 VICQYCEVRLESNS 17 (151)
Q Consensus 4 ~~C~~C~~~f~~~~ 17 (151)
|+|..||..|....
T Consensus 6 y~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 6 YRCEECGHEFEVLQ 19 (42)
T ss_pred EEeCCCCCEEEEEE
Confidence 56777776665443
No 73
>KOG2186|consensus
Probab=88.40 E-value=0.31 Score=34.24 Aligned_cols=49 Identities=22% Similarity=0.491 Sum_probs=31.4
Q ss_pred eeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHHHHHhhhC
Q psy4404 39 YVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHT 92 (151)
Q Consensus 39 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~ 92 (151)
|.| ..||-...- ..+.+|+..-++ .-|.|..|+..|.. ..+..|...=+
T Consensus 4 FtC--nvCgEsvKK-p~vekH~srCrn-~~fSCIDC~k~F~~-~sYknH~kCIT 52 (276)
T KOG2186|consen 4 FTC--NVCGESVKK-PQVEKHMSRCRN-AYFSCIDCGKTFER-VSYKNHTKCIT 52 (276)
T ss_pred Eeh--hhhhhhccc-cchHHHHHhccC-CeeEEeeccccccc-chhhhhhhhcc
Confidence 667 777776655 346667766665 45777778887777 44566655433
No 74
>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=88.31 E-value=0.31 Score=21.31 Aligned_cols=10 Identities=20% Similarity=0.634 Sum_probs=7.0
Q ss_pred ceeecccccc
Q psy4404 2 ILVICQYCEV 11 (151)
Q Consensus 2 ~~~~C~~C~~ 11 (151)
..|+||.||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4677888774
No 75
>KOG2893|consensus
Probab=88.02 E-value=0.14 Score=35.63 Aligned_cols=41 Identities=20% Similarity=0.535 Sum_probs=20.0
Q ss_pred ccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHH
Q psy4404 6 CQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRH 59 (151)
Q Consensus 6 C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h 59 (151)
|=.|++.|..+. -|.+| ...+.|+| ..|.+.+.+--.|..|
T Consensus 13 cwycnrefddek-iliqh----------qkakhfkc--hichkkl~sgpglsih 53 (341)
T KOG2893|consen 13 CWYCNREFDDEK-ILIQH----------QKAKHFKC--HICHKKLFSGPGLSIH 53 (341)
T ss_pred eeecccccchhh-hhhhh----------hhhcccee--eeehhhhccCCCceee
Confidence 444555555554 55555 12234555 5555554444444444
No 76
>KOG2482|consensus
Probab=87.58 E-value=1.5 Score=32.35 Aligned_cols=51 Identities=18% Similarity=0.327 Sum_probs=37.0
Q ss_pred eeCcccccccCChHHHHHHHhhhCC---------------------------CCceeCCcCCccccCHHHHHHHHhhh
Q psy4404 69 FHCPHCEYRCSQQSALYNHLKRHTG---------------------------EKPFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~h~~~h~~---------------------------~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
..|-.|.........|..||..-.. ...-.|-.|...|-....|..||-.+
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vHe~Dl~Ki~sd~~Ln~YqrvrviNyiRkq~~~~~c~~cd~~F~~e~~l~~hm~e~ 357 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVHEFDLLKIQSDYSLNFYQRVRVINYIRKQKKKSRCAECDLSFWKEPGLLIHMVED 357 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHHHhhHHhhccccccchhhhhhHHHHHHHHhhccccccccccccCcchhhhhcccc
Confidence 5788898888888889999864221 01135777888888888888887643
No 77
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.30 E-value=0.38 Score=35.47 Aligned_cols=27 Identities=22% Similarity=0.653 Sum_probs=15.7
Q ss_pred eeeccCCCCcccCCchHHHHHHHhhcC
Q psy4404 39 YVCLYQKCSYHTGNSDHMRRHIRRHTG 65 (151)
Q Consensus 39 ~~C~~~~C~~~f~~~~~l~~h~~~h~~ 65 (151)
|.||...|...-.....|..|.++-++
T Consensus 152 F~CP~skc~~~C~~~k~lk~H~K~~H~ 178 (493)
T COG5236 152 FKCPKSKCHRRCGSLKELKKHYKAQHG 178 (493)
T ss_pred hcCCchhhhhhhhhHHHHHHHHHhhcC
Confidence 666555555555555666666665443
No 78
>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=87.11 E-value=0.49 Score=23.22 Aligned_cols=15 Identities=20% Similarity=0.321 Sum_probs=9.3
Q ss_pred eeeccccccccccCc
Q psy4404 3 LVICQYCEVRLESNS 17 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~ 17 (151)
.|.|+.||..|.-..
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 366777777765433
No 79
>KOG4167|consensus
Probab=87.00 E-value=0.14 Score=41.22 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=20.2
Q ss_pred eeeccccccccccCchHHHHHHhhcC
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCK 28 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~ 28 (151)
.|.|.+|||+|.... .+..||++|.
T Consensus 792 iFpCreC~kvF~KiK-SrNAHMK~Hr 816 (907)
T KOG4167|consen 792 IFPCRECGKVFFKIK-SRNAHMKTHR 816 (907)
T ss_pred eeehHHHHHHHHHHh-hhhHHHHHHH
Confidence 588999999987777 8889987654
No 80
>KOG2231|consensus
Probab=86.57 E-value=1.5 Score=35.44 Aligned_cols=69 Identities=22% Similarity=0.434 Sum_probs=44.9
Q ss_pred eeeccCCCCcccCCchHHHHHHHhhcCCCceeCccc------ccccCChHHHHHHHhhhCCCCceeCC--cCC-ccccCH
Q psy4404 39 YVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHC------EYRCSQQSALYNHLKRHTGEKPFKCT--ICS-HKAARK 109 (151)
Q Consensus 39 ~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C------~~~~~~~~~l~~h~~~h~~~~~~~C~--~C~-~~f~~~ 109 (151)
-.| ..|...|.....|..|++.++ +.|..| +..|..-..|..|.+ +..|.|. .|. +.|...
T Consensus 183 p~C--~~C~~~fld~~el~rH~~~~h----~~chfC~~~~~~neyy~~~~dLe~HfR----~~HflCE~~~C~~~~f~~~ 252 (669)
T KOG2231|consen 183 PLC--KFCHERFLDDDELYRHLRFDH----EFCHFCDYKTGQNEYYNDYDDLEEHFR----KGHFLCEEEFCRTKKFYVA 252 (669)
T ss_pred ccc--hhhhhhhccHHHHHHhhccce----eheeecCcccccchhcccchHHHHHhh----hcCccccccccccceeeeh
Confidence 347 889999999999999998765 345555 455566667777766 4557777 465 234333
Q ss_pred HHHHHHHh
Q psy4404 110 DHMKRHLQ 117 (151)
Q Consensus 110 ~~l~~H~~ 117 (151)
..+..+++
T Consensus 253 ~~~ei~lk 260 (669)
T KOG2231|consen 253 FELEIELK 260 (669)
T ss_pred hHHHHHHH
Confidence 34444444
No 81
>KOG2893|consensus
Probab=86.09 E-value=0.19 Score=35.01 Aligned_cols=39 Identities=18% Similarity=0.384 Sum_probs=19.4
Q ss_pred CCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHHHH
Q psy4404 45 KCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNH 87 (151)
Q Consensus 45 ~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h 87 (151)
.|.+-|.+..-|.+|++.. -|+|.+|.+.+.+-..|..|
T Consensus 15 ycnrefddekiliqhqkak----hfkchichkkl~sgpglsih 53 (341)
T KOG2893|consen 15 YCNREFDDEKILIQHQKAK----HFKCHICHKKLFSGPGLSIH 53 (341)
T ss_pred ecccccchhhhhhhhhhhc----cceeeeehhhhccCCCceee
Confidence 5566666655555554432 25555555444444334433
No 82
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=85.66 E-value=0.56 Score=24.92 Aligned_cols=29 Identities=28% Similarity=0.577 Sum_probs=18.3
Q ss_pred CCCCceeCCcCCccccCHHHHHHHHhhhc
Q psy4404 92 TGEKPFKCTICSHKAARKDHMKRHLQLKH 120 (151)
Q Consensus 92 ~~~~~~~C~~C~~~f~~~~~l~~H~~~~~ 120 (151)
.|+.-+.|+-|+..|....++.+|....+
T Consensus 13 DGE~~lrCPRC~~~FR~~K~Y~RHVNKaH 41 (65)
T COG4049 13 DGEEFLRCPRCGMVFRRRKDYIRHVNKAH 41 (65)
T ss_pred CCceeeeCCchhHHHHHhHHHHHHhhHHh
Confidence 34444667777777777777777766544
No 83
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.56 E-value=1.3 Score=27.40 Aligned_cols=83 Identities=13% Similarity=0.193 Sum_probs=51.0
Q ss_pred eeeccccccccccCchHHHHHHhhcCCC----C--C--CCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCccc
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCKNL----S--R--PDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHC 74 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~----~--~--~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C 74 (151)
|..|+.||.+.-+.. +|..- +|+=. . . ......-.| -.|...|........- .-.....|.|+.|
T Consensus 15 P~~CpiCgLtLVss~-HLARS--yHHLfPl~~f~ev~~~~~~~~~~C--~~C~~~f~~~~~~~~~--~~~~~~~y~C~~C 87 (112)
T TIGR00622 15 PVECPICGLTLILST-HLARS--YHHLFPLKAFQEIPLEEYNGSRFC--FGCQGPFPKPPVSPFD--ELKDSHRYVCAVC 87 (112)
T ss_pred CCcCCcCCCEEeccc-hHHHh--hhccCCCcccccccccccCCCCcc--cCcCCCCCCccccccc--ccccccceeCCCC
Confidence 567999999988877 77643 11100 0 0 001112348 8899999875321100 0122346999999
Q ss_pred ccccCChHHHHHHHhhhC
Q psy4404 75 EYRCSQQSALYNHLKRHT 92 (151)
Q Consensus 75 ~~~~~~~~~l~~h~~~h~ 92 (151)
...|...-+.-.|..+|.
T Consensus 88 ~~~FC~dCD~fiHe~Lh~ 105 (112)
T TIGR00622 88 KNVFCVDCDVFVHESLHC 105 (112)
T ss_pred CCccccccchhhhhhccC
Confidence 999999988888876654
No 84
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=85.48 E-value=0.83 Score=24.30 Aligned_cols=32 Identities=16% Similarity=0.377 Sum_probs=19.8
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCccc
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHT 50 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f 50 (151)
|.|+||.||..+.-.. . .. .....| +.||..+
T Consensus 1 ~~~~CP~CG~~iev~~------------~--~~-GeiV~C--p~CGael 32 (54)
T TIGR01206 1 MQFECPDCGAEIELEN------------P--EL-GELVIC--DECGAEL 32 (54)
T ss_pred CccCCCCCCCEEecCC------------C--cc-CCEEeC--CCCCCEE
Confidence 3578888888774433 1 11 234678 7888664
No 85
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=85.44 E-value=0.42 Score=23.67 Aligned_cols=39 Identities=21% Similarity=0.384 Sum_probs=20.2
Q ss_pred eeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccC
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTG 51 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~ 51 (151)
++|+.||..-.. .++.+.+ ......-..|.| ..|+..|.
T Consensus 1 ~~Cp~C~~~~a~---~~q~Q~R----saDE~mT~fy~C--~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREAT---FFQLQTR----SADEPMTVFYVC--TKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEE---EEEEccc----CCCCCCeEEEEe--CCCCCEeC
Confidence 478889855322 2233311 111111235889 88998764
No 86
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.48 E-value=0.58 Score=25.25 Aligned_cols=34 Identities=21% Similarity=0.653 Sum_probs=19.7
Q ss_pred CcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCccccc
Q psy4404 36 SFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEY 76 (151)
Q Consensus 36 ~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~ 76 (151)
...|.| +.||...-.+-.- -+. ...+|.|+.||.
T Consensus 23 ~~~F~C--PnCG~~~I~RC~~---CRk--~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLC--PNCGEVIIYRCEK---CRK--QSNPYTCPKCGF 56 (59)
T ss_pred cCEeeC--CCCCCeeEeechh---HHh--cCCceECCCCCC
Confidence 345888 8888773333221 111 135789998874
No 87
>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=83.90 E-value=0.7 Score=29.44 Aligned_cols=23 Identities=30% Similarity=0.650 Sum_probs=12.2
Q ss_pred eeccccccccccCchHHHHHHhhcCCC
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNL 30 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~ 30 (151)
.+|-+||+.|+ .|..|.+.|+++
T Consensus 73 i~clecGk~~k----~LkrHL~~~~gl 95 (132)
T PF05443_consen 73 IICLECGKKFK----TLKRHLRTHHGL 95 (132)
T ss_dssp EE-TBT--EES----BHHHHHHHTT-S
T ss_pred eEEccCCcccc----hHHHHHHHccCC
Confidence 56888888884 456776555443
No 88
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=83.69 E-value=1.5 Score=20.77 Aligned_cols=26 Identities=19% Similarity=0.460 Sum_probs=17.8
Q ss_pred ceeeccccccccccCchHHHHHHhhcCC
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKN 29 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~ 29 (151)
..|.|+.|++.+.. .-+..|+..|-+
T Consensus 3 ~~~~C~nC~R~v~a--~RfA~HLekCmg 28 (33)
T PF08209_consen 3 PYVECPNCGRPVAA--SRFAPHLEKCMG 28 (33)
T ss_dssp -EEE-TTTSSEEEG--GGHHHHHHHHTC
T ss_pred CeEECCCCcCCcch--hhhHHHHHHHHc
Confidence 46889999999866 358888666544
No 89
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=83.27 E-value=0.46 Score=26.88 Aligned_cols=44 Identities=11% Similarity=0.163 Sum_probs=27.8
Q ss_pred eeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHH
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHM 56 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l 56 (151)
+.||.||....-+. .-... ....+.-+.|.-..||.+|.....+
T Consensus 2 m~CP~Cg~~a~irt-Sr~~s--------~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHART-SRYIT--------DTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEE-ChhcC--------hhhheeeeecCCCCCCCEEEEEEEE
Confidence 57999998875555 33333 1244556778333899988876543
No 90
>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=82.72 E-value=0.25 Score=24.36 Aligned_cols=38 Identities=16% Similarity=0.357 Sum_probs=17.2
Q ss_pred eeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCccc
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHT 50 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f 50 (151)
++||.||..-... ++.+.+ ......-..|.| ..|+..|
T Consensus 1 ~~Cp~Cg~~~a~~---~~~Q~r----saDE~~T~fy~C--~~C~~~w 38 (39)
T PF01096_consen 1 IKCPKCGHNEAVF---FQIQTR----SADEPMTLFYVC--CNCGHRW 38 (39)
T ss_dssp S--SSS-SSEEEE---EEESSS----SSSSSSEEEEEE--SSSTEEE
T ss_pred CCCcCCCCCeEEE---EEeecc----CCCCCCeEEEEe--CCCCCee
Confidence 4688888763322 222210 111111234888 8898776
No 91
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=82.70 E-value=1.2 Score=28.37 Aligned_cols=23 Identities=30% Similarity=0.394 Sum_probs=17.0
Q ss_pred eeccccccccccCchHHHHHHhhcCCC
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNL 30 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~ 30 (151)
++|.++|+.| |.|..|..+|.++
T Consensus 77 IicLEDGkkf----KSLKRHL~t~~gm 99 (148)
T COG4957 77 IICLEDGKKF----KSLKRHLTTHYGL 99 (148)
T ss_pred EEEeccCcch----HHHHHHHhcccCC
Confidence 5799999999 6788895554443
No 92
>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=82.65 E-value=0.48 Score=31.18 Aligned_cols=34 Identities=18% Similarity=0.474 Sum_probs=20.0
Q ss_pred CCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccC
Q psy4404 35 VSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCS 79 (151)
Q Consensus 35 ~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 79 (151)
....|.| +.|+..|..-.++..- |.|+.||..+.
T Consensus 106 ~~~~Y~C--p~c~~r~tf~eA~~~~---------F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFIC--PNMCVRFTFNEAMELN---------FTCPRCGAMLD 139 (158)
T ss_pred CCCeEEC--CCCCcEeeHHHHHHcC---------CcCCCCCCEee
Confidence 3445667 6677666666665432 56666666543
No 93
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=82.55 E-value=0.53 Score=31.62 Aligned_cols=32 Identities=22% Similarity=0.596 Sum_probs=16.7
Q ss_pred cceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccC
Q psy4404 37 FKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCS 79 (151)
Q Consensus 37 ~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 79 (151)
..|.| +.|+..|..-.++.. . |.|+.||..+.
T Consensus 116 ~~Y~C--p~C~~rytf~eA~~~----~-----F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFC--PNCHIRFTFDEAMEY----G-----FRCPQCGEMLE 147 (178)
T ss_pred CEEEC--CCCCcEEeHHHHhhc----C-----CcCCCCCCCCe
Confidence 44556 556666555555432 1 45666655543
No 94
>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=82.48 E-value=0.93 Score=23.60 Aligned_cols=12 Identities=33% Similarity=0.661 Sum_probs=7.3
Q ss_pred eecccccccccc
Q psy4404 4 VICQYCEVRLES 15 (151)
Q Consensus 4 ~~C~~C~~~f~~ 15 (151)
|+|+.||..|..
T Consensus 6 y~C~~Cg~~fe~ 17 (52)
T TIGR02605 6 YRCTACGHRFEV 17 (52)
T ss_pred EEeCCCCCEeEE
Confidence 556666666643
No 95
>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=82.20 E-value=0.77 Score=20.40 Aligned_cols=19 Identities=21% Similarity=0.412 Sum_probs=12.5
Q ss_pred eeccccccccccCchHHHHHH
Q psy4404 4 VICQYCEVRLESNSKELLEHC 24 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~ 24 (151)
..||.|++.+ ... .+..|.
T Consensus 2 v~CPiC~~~v-~~~-~in~HL 20 (26)
T smart00734 2 VQCPVCFREV-PEN-LINSHL 20 (26)
T ss_pred CcCCCCcCcc-cHH-HHHHHH
Confidence 4678888777 334 677774
No 96
>PF15269 zf-C2H2_7: Zinc-finger
Probab=81.52 E-value=0.85 Score=23.07 Aligned_cols=22 Identities=27% Similarity=0.473 Sum_probs=17.6
Q ss_pred eeccccccccccCchHHHHHHhh
Q psy4404 4 VICQYCEVRLESNSKELLEHCKT 26 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~ 26 (151)
|+|.+|..+-..++ .|..||+.
T Consensus 21 ykcfqcpftc~~ks-hl~nhmky 42 (54)
T PF15269_consen 21 YKCFQCPFTCNEKS-HLFNHMKY 42 (54)
T ss_pred ceeecCCcccchHH-HHHHHHHH
Confidence 56888888887777 89999764
No 97
>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=81.13 E-value=1.3 Score=27.89 Aligned_cols=33 Identities=12% Similarity=0.157 Sum_probs=22.9
Q ss_pred ceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHH
Q psy4404 38 KYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSA 83 (151)
Q Consensus 38 ~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~ 83 (151)
+..| +.||+.|..- ++.|..|+.||..|.....
T Consensus 9 Kr~C--p~cg~kFYDL-----------nk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 9 KRIC--PNTGSKFYDL-----------NRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred cccC--CCcCcccccc-----------CCCCccCCCcCCccCcchh
Confidence 3567 8888888773 3457788888888766543
No 98
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=80.49 E-value=0.75 Score=23.88 Aligned_cols=13 Identities=23% Similarity=0.544 Sum_probs=11.0
Q ss_pred Cceeecccccccc
Q psy4404 1 MILVICQYCEVRL 13 (151)
Q Consensus 1 ~~~~~C~~C~~~f 13 (151)
++.|+|..||+.|
T Consensus 4 ~~~Y~C~~Cg~~~ 16 (49)
T COG1996 4 MMEYKCARCGREV 16 (49)
T ss_pred eEEEEhhhcCCee
Confidence 4788999999988
No 99
>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=79.77 E-value=1.3 Score=21.03 Aligned_cols=8 Identities=63% Similarity=1.431 Sum_probs=3.8
Q ss_pred ceeCCcCC
Q psy4404 96 PFKCTICS 103 (151)
Q Consensus 96 ~~~C~~C~ 103 (151)
|..|+.|+
T Consensus 18 p~~CP~Cg 25 (34)
T cd00729 18 PEKCPICG 25 (34)
T ss_pred CCcCcCCC
Confidence 34455554
No 100
>PHA00626 hypothetical protein
Probab=79.58 E-value=1.8 Score=23.07 Aligned_cols=14 Identities=36% Similarity=0.926 Sum_probs=9.2
Q ss_pred cceeeccCCCCcccCC
Q psy4404 37 FKYVCLYQKCSYHTGN 52 (151)
Q Consensus 37 ~~~~C~~~~C~~~f~~ 52 (151)
..|.| +.||..|..
T Consensus 22 nrYkC--kdCGY~ft~ 35 (59)
T PHA00626 22 DDYVC--CDCGYNDSK 35 (59)
T ss_pred cceEc--CCCCCeech
Confidence 44777 777776654
No 101
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=78.89 E-value=0.78 Score=30.04 Aligned_cols=17 Identities=12% Similarity=0.358 Sum_probs=13.6
Q ss_pred ceeeccCCCCcccCCchHH
Q psy4404 38 KYVCLYQKCSYHTGNSDHM 56 (151)
Q Consensus 38 ~~~C~~~~C~~~f~~~~~l 56 (151)
.+.| +.||.+|.....+
T Consensus 28 ~~~c--~~c~~~f~~~e~~ 44 (154)
T PRK00464 28 RREC--LACGKRFTTFERV 44 (154)
T ss_pred eeec--cccCCcceEeEec
Confidence 4889 8999999887654
No 102
>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=78.53 E-value=1.9 Score=28.33 Aligned_cols=34 Identities=26% Similarity=0.489 Sum_probs=24.5
Q ss_pred hcCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCcc
Q psy4404 63 HTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHK 105 (151)
Q Consensus 63 h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~ 105 (151)
..+..-|.|+.|+..|.....+. .-|.|+.||..
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~---------~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAME---------LNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHH---------cCCcCCCCCCE
Confidence 34456688999998887666543 25899999974
No 103
>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=78.02 E-value=0.83 Score=20.74 Aligned_cols=18 Identities=17% Similarity=0.418 Sum_probs=12.0
Q ss_pred eeccccccccccCchHHHHH
Q psy4404 4 VICQYCEVRLESNSKELLEH 23 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H 23 (151)
|.|-.|++.| ... ..+.|
T Consensus 1 ~sCiDC~~~F-~~~-~y~~H 18 (28)
T PF08790_consen 1 FSCIDCSKDF-DGD-SYKSH 18 (28)
T ss_dssp EEETTTTEEE-EGG-GTTT-
T ss_pred CeeecCCCCc-CcC-CcCCC
Confidence 5688888888 444 66666
No 104
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=77.95 E-value=1.3 Score=21.37 Aligned_cols=13 Identities=23% Similarity=0.478 Sum_probs=7.6
Q ss_pred ceeeccccccccc
Q psy4404 2 ILVICQYCEVRLE 14 (151)
Q Consensus 2 ~~~~C~~C~~~f~ 14 (151)
+.|+|..||....
T Consensus 5 ~~YkC~~CGniVe 17 (36)
T PF06397_consen 5 EFYKCEHCGNIVE 17 (36)
T ss_dssp EEEE-TTT--EEE
T ss_pred cEEEccCCCCEEE
Confidence 5788999988763
No 105
>KOG2785|consensus
Probab=77.86 E-value=2.3 Score=31.82 Aligned_cols=57 Identities=23% Similarity=0.477 Sum_probs=39.5
Q ss_pred eeeccccccccccCchHHHHHHhhcCCCCCCCCCc-----------------ceeeccCCCC---cccCCchHHHHHHHh
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSF-----------------KYVCLYQKCS---YHTGNSDHMRRHIRR 62 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~-----------------~~~C~~~~C~---~~f~~~~~l~~h~~~ 62 (151)
|--|-.|++.|.+.. .-..||..+++..++.-+- .+.| -.|. +.|.+-.+.+.||..
T Consensus 166 Pt~CLfC~~~~k~~e-~~~~HM~~~HgffIPdreYL~D~~GLl~YLgeKV~~~~~C--L~CN~~~~~f~sleavr~HM~~ 242 (390)
T KOG2785|consen 166 PTDCLFCDKKSKSLE-ENLKHMFKEHGFFIPDREYLTDEKGLLKYLGEKVGIGFIC--LFCNELGRPFSSLEAVRAHMRD 242 (390)
T ss_pred CcceeecCCCcccHH-HHHHHHhhccCCcCCchHhhhchhHHHHHHHHHhccCceE--EEeccccCcccccHHHHHHHhh
Confidence 345889999999888 8889998888776655321 2455 3355 667777777777653
No 106
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=77.85 E-value=1.9 Score=28.66 Aligned_cols=24 Identities=42% Similarity=1.029 Sum_probs=17.6
Q ss_pred ceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCc
Q psy4404 68 AFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSH 104 (151)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 104 (151)
.|.|++||..+ -++.|.+|++||-
T Consensus 134 ~~vC~vCGy~~-------------~ge~P~~CPiCga 157 (166)
T COG1592 134 VWVCPVCGYTH-------------EGEAPEVCPICGA 157 (166)
T ss_pred EEEcCCCCCcc-------------cCCCCCcCCCCCC
Confidence 58899997543 4466888999984
No 107
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=77.03 E-value=5.6 Score=25.75 Aligned_cols=38 Identities=18% Similarity=0.512 Sum_probs=24.1
Q ss_pred CCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccc
Q psy4404 65 GEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKA 106 (151)
Q Consensus 65 ~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 106 (151)
+...|.|+.|+..|.....+.. ... ...|.|+.||...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---~d~-~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---LDM-DGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---cCC-CCcEECCCCCCEE
Confidence 4456899999988875443221 112 2338999999744
No 108
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=77.01 E-value=1.2 Score=26.77 Aligned_cols=16 Identities=19% Similarity=0.430 Sum_probs=14.3
Q ss_pred ceeeccccccccccCc
Q psy4404 2 ILVICQYCEVRLESNS 17 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~ 17 (151)
|++.|..||..|..-.
T Consensus 1 MpH~CtrCG~vf~~g~ 16 (112)
T COG3364 1 MPHQCTRCGEVFDDGS 16 (112)
T ss_pred CCceeccccccccccc
Confidence 7899999999998866
No 109
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=76.77 E-value=1.6 Score=22.14 Aligned_cols=14 Identities=29% Similarity=0.570 Sum_probs=9.0
Q ss_pred ceeecccccccccc
Q psy4404 2 ILVICQYCEVRLES 15 (151)
Q Consensus 2 ~~~~C~~C~~~f~~ 15 (151)
+.|+|..||..|.-
T Consensus 1 ~~Y~C~~Cg~~~~~ 14 (44)
T smart00659 1 MIYICGECGRENEI 14 (44)
T ss_pred CEEECCCCCCEeec
Confidence 45777777776643
No 110
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=75.47 E-value=1.4 Score=22.62 Aligned_cols=40 Identities=10% Similarity=0.159 Sum_probs=25.3
Q ss_pred eccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCc
Q psy4404 5 ICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNS 53 (151)
Q Consensus 5 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~ 53 (151)
.||.||....-+. ....+ ....+.-+.|.-..||..|...
T Consensus 1 ~CP~Cg~~a~ir~-S~~~s--------~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRT-SRQLS--------PLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEE-chhhC--------cceEEEEEEECCCcCCCEEEEE
Confidence 4889988876666 44444 1233455778666688887543
No 111
>KOG4173|consensus
Probab=74.73 E-value=0.97 Score=30.91 Aligned_cols=73 Identities=16% Similarity=0.365 Sum_probs=53.0
Q ss_pred eeccc--cccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhc----------CCCceeC
Q psy4404 4 VICQY--CEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHT----------GEKAFHC 71 (151)
Q Consensus 4 ~~C~~--C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~----------~~~~~~C 71 (151)
|.|+. |..+|.+.. .+..| -.+-.+ ..| ..|.+.|++..-|..|+...+ |..-|+|
T Consensus 80 ~~cqvagc~~~~d~lD-~~E~h------Y~~~h~---~sC--s~C~r~~Pt~hLLd~HI~E~HDs~Fqa~veRG~dMy~C 147 (253)
T KOG4173|consen 80 FACQVAGCCQVFDALD-DYEHH------YHTLHG---NSC--SFCKRAFPTGHLLDAHILEWHDSLFQALVERGQDMYQC 147 (253)
T ss_pred ccccccchHHHHhhhh-hHHHh------hhhccc---chh--HHHHHhCCchhhhhHHHHHHHHHHHHHHHHcCccHHHH
Confidence 55776 888888888 78888 333333 358 889999999999988876543 2233777
Q ss_pred cc--cccccCChHHHHHHH
Q psy4404 72 PH--CEYRCSQQSALYNHL 88 (151)
Q Consensus 72 ~~--C~~~~~~~~~l~~h~ 88 (151)
-+ |+..|.....-+.|+
T Consensus 148 lvEgCt~KFkT~r~RkdH~ 166 (253)
T KOG4173|consen 148 LVEGCTEKFKTSRDRKDHM 166 (253)
T ss_pred HHHhhhhhhhhhhhhhhHH
Confidence 54 888888887777776
No 112
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=74.40 E-value=3.2 Score=27.91 Aligned_cols=33 Identities=27% Similarity=0.685 Sum_probs=23.4
Q ss_pred CCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccc
Q psy4404 65 GEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKA 106 (151)
Q Consensus 65 ~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f 106 (151)
...-|.|+.|+..|.....+. .-|.|+.||...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~---------~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAME---------YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhh---------cCCcCCCCCCCC
Confidence 345688999998887665431 258999999743
No 113
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.41 E-value=2.4 Score=24.80 Aligned_cols=11 Identities=18% Similarity=0.815 Sum_probs=6.2
Q ss_pred eeCcccccccC
Q psy4404 69 FHCPHCEYRCS 79 (151)
Q Consensus 69 ~~C~~C~~~~~ 79 (151)
+.|..|+..|.
T Consensus 54 W~C~kCg~~fA 64 (89)
T COG1997 54 WKCRKCGAKFA 64 (89)
T ss_pred EEcCCCCCeec
Confidence 55666655553
No 114
>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=73.22 E-value=4.3 Score=20.20 Aligned_cols=22 Identities=23% Similarity=0.546 Sum_probs=11.1
Q ss_pred eeeccccccccccC---chHHHHHH
Q psy4404 3 LVICQYCEVRLESN---SKELLEHC 24 (151)
Q Consensus 3 ~~~C~~C~~~f~~~---~~~l~~H~ 24 (151)
..+|..|++.+... ...|..|+
T Consensus 16 ~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 16 KAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp -EEETTTTEE-----SSTHHHHHHH
T ss_pred eEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 34677777777663 24677775
No 115
>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=71.80 E-value=2 Score=19.09 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=6.3
Q ss_pred eccccccccc
Q psy4404 5 ICQYCEVRLE 14 (151)
Q Consensus 5 ~C~~C~~~f~ 14 (151)
.|+.||-.|.
T Consensus 16 ~Cp~CG~~F~ 25 (26)
T PF10571_consen 16 FCPHCGYDFE 25 (26)
T ss_pred cCCCCCCCCc
Confidence 4667776664
No 116
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=71.54 E-value=2.1 Score=23.00 Aligned_cols=14 Identities=29% Similarity=0.555 Sum_probs=6.6
Q ss_pred ceeecccccccccc
Q psy4404 2 ILVICQYCEVRLES 15 (151)
Q Consensus 2 ~~~~C~~C~~~f~~ 15 (151)
|..+||.|++.+..
T Consensus 1 m~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 1 MTVKCPICGKPVEW 14 (57)
T ss_dssp -EEE-TTT--EEE-
T ss_pred CcccCCCCCCeecc
Confidence 45678888887655
No 117
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.75 E-value=2.1 Score=24.38 Aligned_cols=10 Identities=30% Similarity=0.673 Sum_probs=5.2
Q ss_pred eecccccccc
Q psy4404 4 VICQYCEVRL 13 (151)
Q Consensus 4 ~~C~~C~~~f 13 (151)
|+|..||..|
T Consensus 13 Y~c~~cg~~~ 22 (82)
T COG2331 13 YECTECGNRF 22 (82)
T ss_pred EeecccchHH
Confidence 4555555543
No 118
>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=70.44 E-value=3 Score=20.09 Aligned_cols=14 Identities=21% Similarity=0.339 Sum_probs=9.4
Q ss_pred eeccccccccccCc
Q psy4404 4 VICQYCEVRLESNS 17 (151)
Q Consensus 4 ~~C~~C~~~f~~~~ 17 (151)
..|+.||++|.-..
T Consensus 2 r~C~~Cg~~Yh~~~ 15 (36)
T PF05191_consen 2 RICPKCGRIYHIEF 15 (36)
T ss_dssp EEETTTTEEEETTT
T ss_pred cCcCCCCCcccccc
Confidence 46888888875444
No 119
>PF12013 DUF3505: Protein of unknown function (DUF3505); InterPro: IPR022698 This family of proteins is functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. This region contains two segments that are likely to be C2H2 zinc binding domains.
Probab=70.41 E-value=4.8 Score=24.50 Aligned_cols=25 Identities=24% Similarity=0.667 Sum_probs=22.9
Q ss_pred eeC----CcCCccccCHHHHHHHHhhhcC
Q psy4404 97 FKC----TICSHKAARKDHMKRHLQLKHN 121 (151)
Q Consensus 97 ~~C----~~C~~~f~~~~~l~~H~~~~~~ 121 (151)
|.| ..|+........+..|.+.+||
T Consensus 81 ~~C~~~~~~C~y~~~~~~~m~~H~~~~Hg 109 (109)
T PF12013_consen 81 YRCQCDPPHCGYITRSKKTMRKHWRKEHG 109 (109)
T ss_pred eeeecCCCCCCcEeccHHHHHHHHHHhcC
Confidence 899 9999999999999999998875
No 120
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=70.24 E-value=2.4 Score=20.84 Aligned_cols=14 Identities=14% Similarity=0.263 Sum_probs=10.2
Q ss_pred eeeccccccccccC
Q psy4404 3 LVICQYCEVRLESN 16 (151)
Q Consensus 3 ~~~C~~C~~~f~~~ 16 (151)
+|+|..|++.|=..
T Consensus 12 ~f~C~~C~~~FC~~ 25 (39)
T smart00154 12 GFKCRHCGNLFCGE 25 (39)
T ss_pred CeECCccCCccccc
Confidence 67888888887543
No 121
>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=70.23 E-value=1.9 Score=21.59 Aligned_cols=13 Identities=15% Similarity=0.314 Sum_probs=6.0
Q ss_pred eeecccccccccc
Q psy4404 3 LVICQYCEVRLES 15 (151)
Q Consensus 3 ~~~C~~C~~~f~~ 15 (151)
+|+|+.|++.|=.
T Consensus 13 ~~~C~~C~~~FC~ 25 (43)
T PF01428_consen 13 PFKCKHCGKSFCL 25 (43)
T ss_dssp HEE-TTTS-EE-T
T ss_pred CeECCCCCcccCc
Confidence 4566666666643
No 122
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=70.21 E-value=4.2 Score=20.18 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=15.2
Q ss_pred eeccccccccccCc-hHHHHHHhh
Q psy4404 4 VICQYCEVRLESNS-KELLEHCKT 26 (151)
Q Consensus 4 ~~C~~C~~~f~~~~-~~l~~H~~~ 26 (151)
.+|+.||..|.... .+-..|.+.
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~y 37 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKY 37 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHH
Confidence 47899998886655 355566443
No 123
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=69.17 E-value=3.3 Score=19.49 Aligned_cols=13 Identities=23% Similarity=0.511 Sum_probs=9.7
Q ss_pred ceeeccccccccc
Q psy4404 2 ILVICQYCEVRLE 14 (151)
Q Consensus 2 ~~~~C~~C~~~f~ 14 (151)
+.|+|..||....
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 5788888887764
No 124
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=68.69 E-value=2.8 Score=26.60 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=13.2
Q ss_pred eeeccccccccccCc
Q psy4404 3 LVICQYCEVRLESNS 17 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~ 17 (151)
|++|..||+.|...+
T Consensus 1 PH~Ct~Cg~~f~dgs 15 (131)
T PF09845_consen 1 PHQCTKCGRVFEDGS 15 (131)
T ss_pred CcccCcCCCCcCCCc
Confidence 578999999998876
No 125
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=68.45 E-value=4.4 Score=20.88 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=14.5
Q ss_pred eeccccccccccCc----hHHHHHHh
Q psy4404 4 VICQYCEVRLESNS----KELLEHCK 25 (151)
Q Consensus 4 ~~C~~C~~~f~~~~----~~l~~H~~ 25 (151)
-.|..|++.+.... +.|..|++
T Consensus 19 a~C~~C~~~l~~~~~~gTs~L~rHl~ 44 (50)
T smart00614 19 AKCKYCGKKLSRSSKGGTSNLRRHLR 44 (50)
T ss_pred EEecCCCCEeeeCCCCCcHHHHHHHH
Confidence 45888888876541 37777754
No 126
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=67.70 E-value=2.7 Score=24.95 Aligned_cols=12 Identities=50% Similarity=1.226 Sum_probs=10.5
Q ss_pred Cceeeccccccc
Q psy4404 1 MILVICQYCEVR 12 (151)
Q Consensus 1 ~~~~~C~~C~~~ 12 (151)
|+++.||.||..
T Consensus 1 mlLI~CP~Cg~R 12 (97)
T COG4311 1 MLLIPCPYCGER 12 (97)
T ss_pred CceecCCCCCCC
Confidence 788999999983
No 127
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=66.87 E-value=15 Score=27.47 Aligned_cols=74 Identities=22% Similarity=0.356 Sum_probs=49.5
Q ss_pred eeccCCCCcccCCchHHHHHHHhhcCCCceeCcc----cccccCChHHHHHHHhhhCCCCceeCCc--CC----ccccCH
Q psy4404 40 VCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPH----CEYRCSQQSALYNHLKRHTGEKPFKCTI--CS----HKAARK 109 (151)
Q Consensus 40 ~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~----C~~~~~~~~~l~~h~~~h~~~~~~~C~~--C~----~~f~~~ 109 (151)
.| ..|...|.+-+.|..|++..++ +.+.|.. -..-|..-..|-.|.+ .-.|.|.. |. ..|...
T Consensus 222 ~C--~FC~~~FYdDDEL~~HcR~~HE-~ChICD~v~p~~~QYFK~Y~~Le~HF~----~~hy~ct~qtc~~~k~~vf~~~ 294 (493)
T COG5236 222 LC--IFCKIYFYDDDELRRHCRLRHE-ACHICDMVGPIRYQYFKSYEDLEAHFR----NAHYCCTFQTCRVGKCYVFPYH 294 (493)
T ss_pred hh--hhccceecChHHHHHHHHhhhh-hhhhhhccCccchhhhhCHHHHHHHhh----cCceEEEEEEEecCcEEEeccH
Confidence 47 8899999999999999988664 3455543 2233455555665544 34566643 32 367888
Q ss_pred HHHHHHHhhhc
Q psy4404 110 DHMKRHLQLKH 120 (151)
Q Consensus 110 ~~l~~H~~~~~ 120 (151)
..|..|+...+
T Consensus 295 ~el~~h~~~~h 305 (493)
T COG5236 295 TELLEHLTRFH 305 (493)
T ss_pred HHHHHHHHHHh
Confidence 88999987655
No 128
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=66.48 E-value=4 Score=19.16 Aligned_cols=13 Identities=23% Similarity=0.521 Sum_probs=9.8
Q ss_pred ceeeccccccccc
Q psy4404 2 ILVICQYCEVRLE 14 (151)
Q Consensus 2 ~~~~C~~C~~~f~ 14 (151)
+.|+|..||....
T Consensus 6 ~~ykC~~Cgniv~ 18 (34)
T TIGR00319 6 QVYKCEVCGNIVE 18 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 4788888888763
No 129
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=66.32 E-value=4.4 Score=25.91 Aligned_cols=13 Identities=15% Similarity=0.498 Sum_probs=7.5
Q ss_pred eeecccccccccc
Q psy4404 3 LVICQYCEVRLES 15 (151)
Q Consensus 3 ~~~C~~C~~~f~~ 15 (151)
.+.|+.||..|..
T Consensus 70 ~~~C~~CG~~~~~ 82 (135)
T PRK03824 70 VLKCRNCGNEWSL 82 (135)
T ss_pred EEECCCCCCEEec
Confidence 3556666666544
No 130
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=66.26 E-value=3.5 Score=25.51 Aligned_cols=12 Identities=33% Similarity=0.911 Sum_probs=6.6
Q ss_pred ceeeccCCCCcccC
Q psy4404 38 KYVCLYQKCSYHTG 51 (151)
Q Consensus 38 ~~~C~~~~C~~~f~ 51 (151)
.|.| ..||..|.
T Consensus 100 Fy~C--~~Cg~~wr 111 (113)
T COG1594 100 FYKC--TRCGYRWR 111 (113)
T ss_pred EEEe--cccCCEee
Confidence 3556 55665554
No 131
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=65.72 E-value=3.7 Score=21.33 Aligned_cols=16 Identities=13% Similarity=0.378 Sum_probs=10.6
Q ss_pred ceeeccccccccccCc
Q psy4404 2 ILVICQYCEVRLESNS 17 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~ 17 (151)
+.+.|..||..|.-..
T Consensus 3 k~l~C~dCg~~FvfTa 18 (49)
T PF13451_consen 3 KTLTCKDCGAEFVFTA 18 (49)
T ss_pred eeEEcccCCCeEEEeh
Confidence 5667777777765544
No 132
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=64.55 E-value=8.6 Score=27.91 Aligned_cols=37 Identities=30% Similarity=0.520 Sum_probs=30.6
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCccee
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYV 40 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~ 40 (151)
.+|+|..|=+-|.++. .|..|+..|.-. .+.|...|+
T Consensus 47 ~lyiCe~Clky~~~~~-~l~~H~~~C~~r-~PPG~eIYr 83 (290)
T PLN03238 47 KLYICEYCLKYMRKKK-SLLRHLAKCDIR-QPPGGGIYG 83 (290)
T ss_pred eEEEcCCCcchhCCHH-HHHHHHHhCCCC-CCCcCEeEe
Confidence 6899999999999999 999998877654 456777776
No 133
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=64.18 E-value=7.9 Score=28.92 Aligned_cols=31 Identities=29% Similarity=0.517 Sum_probs=24.1
Q ss_pred HhhhCCCCceeCCcCC-ccccCHHHHHHHHhh
Q psy4404 88 LKRHTGEKPFKCTICS-HKAARKDHMKRHLQL 118 (151)
Q Consensus 88 ~~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~~ 118 (151)
.+.|.-.+.|.|.+|| +.+.-+..+-+|...
T Consensus 366 ~klhgLd~ef~CEICgNyvy~GR~~FdrHF~E 397 (470)
T COG5188 366 CKLHGLDIEFECEICGNYVYYGRDRFDRHFEE 397 (470)
T ss_pred HHhcCCCcceeeeecccccccchHHHHhhhhh
Confidence 3567777889999999 677777888888653
No 134
>KOG3408|consensus
Probab=64.02 E-value=3.3 Score=25.82 Aligned_cols=23 Identities=26% Similarity=0.359 Sum_probs=17.0
Q ss_pred eeeccccccccccCchHHHHHHhh
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKT 26 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~ 26 (151)
.|-|-+|.+.|.+.. .|+.|.++
T Consensus 57 qfyCi~CaRyFi~~~-~l~~H~kt 79 (129)
T KOG3408|consen 57 QFYCIECARYFIDAK-ALKTHFKT 79 (129)
T ss_pred eeehhhhhhhhcchH-HHHHHHhc
Confidence 467888888887777 88888443
No 135
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=63.54 E-value=5.6 Score=20.13 Aligned_cols=9 Identities=22% Similarity=0.962 Sum_probs=5.3
Q ss_pred CceeCcccc
Q psy4404 67 KAFHCPHCE 75 (151)
Q Consensus 67 ~~~~C~~C~ 75 (151)
..|.|..|+
T Consensus 36 ~~~~C~~C~ 44 (46)
T PF12760_consen 36 GRYRCKACR 44 (46)
T ss_pred CeEECCCCC
Confidence 446666664
No 136
>PF14353 CpXC: CpXC protein
Probab=63.44 E-value=2 Score=27.00 Aligned_cols=20 Identities=25% Similarity=0.472 Sum_probs=15.4
Q ss_pred eeeccccccccccCchHHHHH
Q psy4404 3 LVICQYCEVRLESNSKELLEH 23 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H 23 (151)
.|.||.||..|.-.. .+..|
T Consensus 38 ~~~CP~Cg~~~~~~~-p~lY~ 57 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEY-PLLYH 57 (128)
T ss_pred EEECCCCCCceecCC-CEEEE
Confidence 577888888887777 77776
No 137
>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=62.04 E-value=4.5 Score=28.07 Aligned_cols=32 Identities=19% Similarity=0.366 Sum_probs=23.2
Q ss_pred CCCCCcceeeccCCCCcccCCchHHHHHHHhhcC
Q psy4404 32 RPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTG 65 (151)
Q Consensus 32 ~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~ 65 (151)
...++..|.| +.|++.|.-...+.+|+..-+.
T Consensus 71 ~e~~~~K~~C--~lc~KlFkg~eFV~KHI~nKH~ 102 (214)
T PF04959_consen 71 KEEDEDKWRC--PLCGKLFKGPEFVRKHIFNKHP 102 (214)
T ss_dssp -SSSSEEEEE---SSS-EESSHHHHHHHHHHH-H
T ss_pred HHHcCCEECC--CCCCcccCChHHHHHHHhhcCH
Confidence 3456667999 8999999999999999876544
No 138
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=61.32 E-value=18 Score=19.05 Aligned_cols=18 Identities=28% Similarity=0.650 Sum_probs=8.2
Q ss_pred HHHHHhhhCCCCceeCCc
Q psy4404 84 LYNHLKRHTGEKPFKCTI 101 (151)
Q Consensus 84 l~~h~~~h~~~~~~~C~~ 101 (151)
|..|.......++..|..
T Consensus 26 l~~H~~~~C~~~~v~C~~ 43 (60)
T PF02176_consen 26 LDDHLENECPKRPVPCPY 43 (60)
T ss_dssp HHHHHHTTSTTSEEE-SS
T ss_pred HHHHHHccCCCCcEECCC
Confidence 455554444444445555
No 139
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=60.41 E-value=6.3 Score=18.99 Aligned_cols=31 Identities=23% Similarity=0.519 Sum_probs=19.8
Q ss_pred eeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCC
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKC 46 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C 46 (151)
...||.|+..- .+..| -....|...|.| ..|
T Consensus 5 ~v~CP~C~s~~-----~v~k~------G~~~~G~qryrC--~~C 35 (36)
T PF03811_consen 5 DVHCPRCQSTE-----GVKKN------GKSPSGHQRYRC--KDC 35 (36)
T ss_pred eeeCCCCCCCC-----cceeC------CCCCCCCEeEec--CcC
Confidence 35688887652 24445 556677777888 776
No 140
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=60.17 E-value=5.1 Score=21.44 Aligned_cols=41 Identities=20% Similarity=0.417 Sum_probs=20.8
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCccc
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHT 50 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f 50 (151)
|-.+|..||+.+.=....+..- ...-.....|.| +.|....
T Consensus 1 m~vkC~lCdk~~~Id~~~~~aK------rLrnrPi~tYmC--~eC~~RI 41 (56)
T PF09963_consen 1 MRVKCILCDKKEEIDEDTPEAK------RLRNRPIHTYMC--DECKERI 41 (56)
T ss_pred CeeEEEecCCEEEeccCCHHHH------HhhcCCCcceeC--hhHHHHH
Confidence 3457777887764433223322 111123445777 7776543
No 141
>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=60.06 E-value=5.6 Score=27.62 Aligned_cols=29 Identities=21% Similarity=0.591 Sum_probs=18.4
Q ss_pred CCceeCCcCCccccCHHHHHHHHhhhcCC
Q psy4404 94 EKPFKCTICSHKAARKDHMKRHLQLKHNA 122 (151)
Q Consensus 94 ~~~~~C~~C~~~f~~~~~l~~H~~~~~~~ 122 (151)
+..|.|..|+|.|.-..-.+.|+...|.+
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e 103 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPE 103 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHH
Confidence 33477888888888777777777766543
No 142
>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=58.36 E-value=4.1 Score=21.38 Aligned_cols=20 Identities=20% Similarity=0.748 Sum_probs=7.1
Q ss_pred ceeCcccccccCChHHHHHH
Q psy4404 68 AFHCPHCEYRCSQQSALYNH 87 (151)
Q Consensus 68 ~~~C~~C~~~~~~~~~l~~h 87 (151)
.|.|+.|...|-..=+.-.|
T Consensus 21 ~y~C~~C~~~FC~dCD~fiH 40 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIH 40 (51)
T ss_dssp EE--TTTT--B-HHHHHTTT
T ss_pred eEECCCCCCccccCcChhhh
Confidence 35555555555444444433
No 143
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=56.93 E-value=11 Score=19.23 Aligned_cols=13 Identities=38% Similarity=1.101 Sum_probs=8.4
Q ss_pred ceeeccCCCCcccCC
Q psy4404 38 KYVCLYQKCSYHTGN 52 (151)
Q Consensus 38 ~~~C~~~~C~~~f~~ 52 (151)
.+.| +.||..+..
T Consensus 20 ~~vC--~~Cg~~~~~ 32 (52)
T smart00661 20 RFVC--RKCGYEEPI 32 (52)
T ss_pred EEEC--CcCCCeEEC
Confidence 5677 777765544
No 144
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=56.49 E-value=5 Score=20.07 Aligned_cols=13 Identities=23% Similarity=0.539 Sum_probs=7.5
Q ss_pred eccccccccccCc
Q psy4404 5 ICQYCEVRLESNS 17 (151)
Q Consensus 5 ~C~~C~~~f~~~~ 17 (151)
+|+.||+.|.-+.
T Consensus 10 ~C~~C~rpf~WRK 22 (42)
T PF10013_consen 10 ICPVCGRPFTWRK 22 (42)
T ss_pred cCcccCCcchHHH
Confidence 3666666665443
No 145
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=56.13 E-value=6.4 Score=19.50 Aligned_cols=11 Identities=45% Similarity=1.171 Sum_probs=8.2
Q ss_pred eeecccccccc
Q psy4404 3 LVICQYCEVRL 13 (151)
Q Consensus 3 ~~~C~~C~~~f 13 (151)
+..|+.||..|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 46788888776
No 146
>PF12907 zf-met2: Zinc-binding
Probab=56.02 E-value=3.8 Score=20.29 Aligned_cols=21 Identities=29% Similarity=0.713 Sum_probs=14.2
Q ss_pred eeccccccccccCc--hHHHHHH
Q psy4404 4 VICQYCEVRLESNS--KELLEHC 24 (151)
Q Consensus 4 ~~C~~C~~~f~~~~--~~l~~H~ 24 (151)
++|.+|-..|.... +.|..|.
T Consensus 2 i~C~iC~qtF~~t~~~~~L~eH~ 24 (40)
T PF12907_consen 2 IICKICRQTFMQTTNEPQLKEHA 24 (40)
T ss_pred cCcHHhhHHHHhcCCHHHHHHHH
Confidence 56888886665544 3688885
No 147
>KOG2807|consensus
Probab=55.28 E-value=28 Score=25.91 Aligned_cols=25 Identities=16% Similarity=0.323 Sum_probs=18.7
Q ss_pred CceeCCcCCccccCHHHHHHHHhhh
Q psy4404 95 KPFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 95 ~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
..|.|..|...|-..-+.-.|-..|
T Consensus 344 ~~y~C~~Ck~~FCldCDv~iHesLh 368 (378)
T KOG2807|consen 344 GRYRCESCKNVFCLDCDVFIHESLH 368 (378)
T ss_pred CcEEchhccceeeccchHHHHhhhh
Confidence 3588888888888777777776665
No 148
>PTZ00064 histone acetyltransferase; Provisional
Probab=54.75 E-value=15 Score=29.00 Aligned_cols=38 Identities=26% Similarity=0.428 Sum_probs=31.5
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceee
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVC 41 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C 41 (151)
++|+|..|=+-|.+.. .|..|+..|... .+.|...|+.
T Consensus 279 ~LYICEfCLkY~~s~~-~l~rH~~~C~~r-hPPG~EIYR~ 316 (552)
T PTZ00064 279 TLHFCEYCLDFFCFED-ELIRHLSRCQLR-HPPGNEIYRK 316 (552)
T ss_pred eEEEccchhhhhCCHH-HHHHHHhcCCCC-CCCCCeEEEe
Confidence 6899999999999999 999998877654 4567777876
No 149
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=54.56 E-value=9.6 Score=18.10 Aligned_cols=13 Identities=23% Similarity=0.703 Sum_probs=8.1
Q ss_pred CcceeeccCCCCccc
Q psy4404 36 SFKYVCLYQKCSYHT 50 (151)
Q Consensus 36 ~~~~~C~~~~C~~~f 50 (151)
...+.| +.||...
T Consensus 20 r~R~vC--~~Cg~Ih 32 (34)
T PF14803_consen 20 RERLVC--PACGFIH 32 (34)
T ss_dssp S-EEEE--TTTTEEE
T ss_pred ccceEC--CCCCCEE
Confidence 345778 7888653
No 150
>KOG3408|consensus
Probab=54.40 E-value=9.5 Score=23.87 Aligned_cols=27 Identities=26% Similarity=0.517 Sum_probs=21.2
Q ss_pred CCCceeCCcCCccccCHHHHHHHHhhh
Q psy4404 93 GEKPFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 93 ~~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
|.-.|.|..|.+-|.....|..|.++.
T Consensus 54 G~GqfyCi~CaRyFi~~~~l~~H~ktK 80 (129)
T KOG3408|consen 54 GGGQFYCIECARYFIDAKALKTHFKTK 80 (129)
T ss_pred CCceeehhhhhhhhcchHHHHHHHhcc
Confidence 333488888999999999998888764
No 151
>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=54.18 E-value=5.5 Score=20.90 Aligned_cols=13 Identities=23% Similarity=0.657 Sum_probs=6.0
Q ss_pred eccccccccccCc
Q psy4404 5 ICQYCEVRLESNS 17 (151)
Q Consensus 5 ~C~~C~~~f~~~~ 17 (151)
.||.|++.|....
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 6888888776543
No 152
>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=53.12 E-value=5.3 Score=28.52 Aligned_cols=84 Identities=15% Similarity=0.345 Sum_probs=45.2
Q ss_pred CCCcceeeccCCCCcccCCchHHHHHHHhh--cCCCceeCcccccccCChH------HHHHHHhh----hCCCCceeCCc
Q psy4404 34 DVSFKYVCLYQKCSYHTGNSDHMRRHIRRH--TGEKAFHCPHCEYRCSQQS------ALYNHLKR----HTGEKPFKCTI 101 (151)
Q Consensus 34 ~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h--~~~~~~~C~~C~~~~~~~~------~l~~h~~~----h~~~~~~~C~~ 101 (151)
.|.+.|.| ..|...+..-..+ .|+.+- .....|+|.-|++.-...- .--.|.+. ....+++.|+.
T Consensus 138 hGGrif~C--sfC~~flCEDDQF-EHQAsCQvLe~E~~KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPK 214 (314)
T PF06524_consen 138 HGGRIFKC--SFCDNFLCEDDQF-EHQASCQVLESETFKCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPK 214 (314)
T ss_pred CCCeEEEe--ecCCCeeeccchh-hhhhhhhhhhcccccccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCC
Confidence 45567888 7788755544443 333321 1122355555554322110 01233332 23346789999
Q ss_pred CCccccCHHHHHHHHhhhc
Q psy4404 102 CSHKAARKDHMKRHLQLKH 120 (151)
Q Consensus 102 C~~~f~~~~~l~~H~~~~~ 120 (151)
|+........|.-..|+|.
T Consensus 215 Cg~et~eTkdLSmStR~hk 233 (314)
T PF06524_consen 215 CGYETQETKDLSMSTRSHK 233 (314)
T ss_pred CCCcccccccceeeeecch
Confidence 9987777777766666654
No 153
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=52.80 E-value=15 Score=28.48 Aligned_cols=38 Identities=24% Similarity=0.454 Sum_probs=31.4
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceee
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVC 41 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C 41 (151)
.+|+|..|=+-|.+.. .|..|+..|... .+.|...|+.
T Consensus 197 ~lyiCe~Cl~y~~~~~-~~~~H~~~C~~~-~PPG~eIYr~ 234 (450)
T PLN00104 197 KLYFCEFCLKFMKRKE-QLQRHMKKCDLK-HPPGDEIYRH 234 (450)
T ss_pred eEEEchhhhhhhcCHH-HHHHHHhcCCCC-CCCcCeEEEc
Confidence 5899999999999999 999998777644 4567777876
No 154
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=52.45 E-value=13 Score=18.38 Aligned_cols=10 Identities=20% Similarity=0.634 Sum_probs=6.1
Q ss_pred eecccccccc
Q psy4404 4 VICQYCEVRL 13 (151)
Q Consensus 4 ~~C~~C~~~f 13 (151)
|+||.||...
T Consensus 1 m~Cp~Cg~~~ 10 (43)
T PF08271_consen 1 MKCPNCGSKE 10 (43)
T ss_dssp ESBTTTSSSE
T ss_pred CCCcCCcCCc
Confidence 4567776653
No 155
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=51.99 E-value=5.8 Score=23.92 Aligned_cols=11 Identities=27% Similarity=0.941 Sum_probs=6.4
Q ss_pred ceeCccccccc
Q psy4404 68 AFHCPHCEYRC 78 (151)
Q Consensus 68 ~~~C~~C~~~~ 78 (151)
-|.|..|+..+
T Consensus 90 fy~C~~C~~~w 100 (104)
T TIGR01384 90 FYKCTKCGYVW 100 (104)
T ss_pred EEEeCCCCCee
Confidence 36666666544
No 156
>KOG2593|consensus
Probab=51.80 E-value=10 Score=29.12 Aligned_cols=39 Identities=21% Similarity=0.435 Sum_probs=23.1
Q ss_pred CCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCccccccc
Q psy4404 35 VSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRC 78 (151)
Q Consensus 35 ~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~ 78 (151)
....|.| +.|.+.|.+-..+ +..-.....|.|..|+.-.
T Consensus 125 ~~~~Y~C--p~C~kkyt~Lea~---~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 125 NVAGYVC--PNCQKKYTSLEAL---QLLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccccC--CccccchhhhHHH---HhhcccCceEEEecCCCch
Confidence 3445778 7788777665543 2233334457777776554
No 157
>PHA02998 RNA polymerase subunit; Provisional
Probab=50.56 E-value=7.5 Score=26.08 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=6.2
Q ss_pred eeeccCCCCcccC
Q psy4404 39 YVCLYQKCSYHTG 51 (151)
Q Consensus 39 ~~C~~~~C~~~f~ 51 (151)
|.| ..||..|.
T Consensus 172 YkC--~~CG~~wk 182 (195)
T PHA02998 172 HAC--RDCKKHFK 182 (195)
T ss_pred EEc--CCCCCccC
Confidence 556 55665554
No 158
>KOG2907|consensus
Probab=50.16 E-value=13 Score=22.99 Aligned_cols=10 Identities=40% Similarity=1.560 Sum_probs=5.1
Q ss_pred eeCccccccc
Q psy4404 69 FHCPHCEYRC 78 (151)
Q Consensus 69 ~~C~~C~~~~ 78 (151)
|.|+.|+..|
T Consensus 103 YTC~kC~~k~ 112 (116)
T KOG2907|consen 103 YTCPKCKYKF 112 (116)
T ss_pred EEcCccceee
Confidence 5555555444
No 159
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=49.43 E-value=5.5 Score=27.78 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=0.0
Q ss_pred eeeccccccccccCchHHHHHHhh
Q psy4404 3 LVICQYCEVRLESNSKELLEHCKT 26 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~~~ 26 (151)
..+||.||+..-. ..|..|||+
T Consensus 168 ~~~cPitGe~IP~--~e~~eHmRi 189 (229)
T PF12230_consen 168 MIICPITGEMIPA--DEMDEHMRI 189 (229)
T ss_dssp ------------------------
T ss_pred ccccccccccccc--ccccccccc
Confidence 4568888887755 367778654
No 160
>KOG2482|consensus
Probab=49.07 E-value=16 Score=27.32 Aligned_cols=24 Identities=17% Similarity=0.449 Sum_probs=19.3
Q ss_pred eeCCcCCccccCHHHHHHHHhhhc
Q psy4404 97 FKCTICSHKAARKDHMKRHLQLKH 120 (151)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~~ 120 (151)
..|..|....-....|..||++.|
T Consensus 280 v~CLfC~~~~en~~~l~eHmk~vH 303 (423)
T KOG2482|consen 280 VVCLFCTNFYENPVFLFEHMKIVH 303 (423)
T ss_pred eEEEeeccchhhHHHHHHHHHHHH
Confidence 578888887777888888888766
No 161
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=48.95 E-value=15 Score=19.08 Aligned_cols=11 Identities=36% Similarity=1.144 Sum_probs=5.7
Q ss_pred ceeeccCCCCccc
Q psy4404 38 KYVCLYQKCSYHT 50 (151)
Q Consensus 38 ~~~C~~~~C~~~f 50 (151)
.+.| +.||..+
T Consensus 37 r~~C--~~Cgyt~ 47 (50)
T PRK00432 37 RWHC--GKCGYTE 47 (50)
T ss_pred cEEC--CCcCCEE
Confidence 3556 5565543
No 162
>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=48.61 E-value=9.1 Score=17.91 Aligned_cols=11 Identities=36% Similarity=0.827 Sum_probs=6.1
Q ss_pred eeccccccccc
Q psy4404 4 VICQYCEVRLE 14 (151)
Q Consensus 4 ~~C~~C~~~f~ 14 (151)
|+|..||..+.
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 45666666654
No 163
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=47.75 E-value=7.5 Score=22.51 Aligned_cols=11 Identities=18% Similarity=0.534 Sum_probs=4.9
Q ss_pred eeCcccccccC
Q psy4404 69 FHCPHCEYRCS 79 (151)
Q Consensus 69 ~~C~~C~~~~~ 79 (151)
..|..|+..|.
T Consensus 47 ~~C~~Cg~~~~ 57 (81)
T PF05129_consen 47 LSCRVCGESFQ 57 (81)
T ss_dssp EEESSS--EEE
T ss_pred EEecCCCCeEE
Confidence 45666655553
No 164
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=46.99 E-value=19 Score=23.05 Aligned_cols=17 Identities=18% Similarity=0.307 Sum_probs=10.5
Q ss_pred CCCcceeeccCCCCcccCC
Q psy4404 34 DVSFKYVCLYQKCSYHTGN 52 (151)
Q Consensus 34 ~~~~~~~C~~~~C~~~f~~ 52 (151)
.+.+-|.| +.|..+...
T Consensus 76 ~d~~lYeC--nIC~etS~e 92 (140)
T PF05290_consen 76 LDPKLYEC--NICKETSAE 92 (140)
T ss_pred cCCCceec--cCcccccch
Confidence 34466777 777765444
No 165
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.54 E-value=14 Score=22.70 Aligned_cols=26 Identities=4% Similarity=-0.033 Sum_probs=17.4
Q ss_pred CCCCcccCCchHHHHHHHhhcCCCceeCcccccccCC
Q psy4404 44 QKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQ 80 (151)
Q Consensus 44 ~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 80 (151)
+.||+.|..- +..|..|+.||+.|+.
T Consensus 13 Petg~KFYDL-----------NrdPiVsPytG~s~P~ 38 (129)
T COG4530 13 PETGKKFYDL-----------NRDPIVSPYTGKSYPR 38 (129)
T ss_pred ccccchhhcc-----------CCCccccCcccccchH
Confidence 7777777662 3456777888877743
No 166
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=45.48 E-value=12 Score=17.56 Aligned_cols=11 Identities=18% Similarity=0.815 Sum_probs=7.1
Q ss_pred eeccccccccc
Q psy4404 4 VICQYCEVRLE 14 (151)
Q Consensus 4 ~~C~~C~~~f~ 14 (151)
+.|..||.+|.
T Consensus 22 ~~C~~Cg~~~~ 32 (33)
T PF08792_consen 22 EVCIFCGSSFP 32 (33)
T ss_pred EEcccCCcEee
Confidence 45777777663
No 167
>KOG4167|consensus
Probab=45.42 E-value=5.2 Score=32.78 Aligned_cols=27 Identities=15% Similarity=0.294 Sum_probs=23.1
Q ss_pred cceeeccCCCCcccCCchHHHHHHHhhcC
Q psy4404 37 FKYVCLYQKCSYHTGNSDHMRRHIRRHTG 65 (151)
Q Consensus 37 ~~~~C~~~~C~~~f~~~~~l~~h~~~h~~ 65 (151)
..|.| .+|++.|....++..||+.|.-
T Consensus 791 giFpC--reC~kvF~KiKSrNAHMK~Hr~ 817 (907)
T KOG4167|consen 791 GIFPC--RECGKVFFKIKSRNAHMKTHRQ 817 (907)
T ss_pred ceeeh--HHHHHHHHHHhhhhHHHHHHHH
Confidence 35889 8999999999999999998854
No 168
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=45.12 E-value=5 Score=22.54 Aligned_cols=13 Identities=15% Similarity=0.368 Sum_probs=5.3
Q ss_pred ceeCcccccccCC
Q psy4404 68 AFHCPHCEYRCSQ 80 (151)
Q Consensus 68 ~~~C~~C~~~~~~ 80 (151)
...|..|+..+..
T Consensus 41 ~v~Cg~C~~~~~~ 53 (71)
T PF05495_consen 41 RVICGKCRTEQPI 53 (71)
T ss_dssp EEEETTT--EEES
T ss_pred CeECCCCCCccCh
Confidence 3455555544433
No 169
>KOG2747|consensus
Probab=45.05 E-value=19 Score=27.49 Aligned_cols=36 Identities=33% Similarity=0.588 Sum_probs=28.0
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcce
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKY 39 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~ 39 (151)
++|+|..|=+-+.+.. .|+.|+..|.-. .+.|...|
T Consensus 157 ~lYiCEfCLkY~~s~~-~l~rH~~kC~~r-hPPG~EIY 192 (396)
T KOG2747|consen 157 KLYICEFCLKYMKSRT-SLQRHLKKCKLR-HPPGNEIY 192 (396)
T ss_pred eEEEehHHHhHhchHH-HHHHHHHhcCCC-CCCcceee
Confidence 6899999999999999 999998887744 33444433
No 170
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.91 E-value=10 Score=20.87 Aligned_cols=11 Identities=27% Similarity=0.552 Sum_probs=6.1
Q ss_pred eeccccccccc
Q psy4404 4 VICQYCEVRLE 14 (151)
Q Consensus 4 ~~C~~C~~~f~ 14 (151)
.+||.||+.-.
T Consensus 8 v~CP~Cgkpv~ 18 (65)
T COG3024 8 VPCPTCGKPVV 18 (65)
T ss_pred ccCCCCCCccc
Confidence 45666666543
No 171
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=44.88 E-value=9.5 Score=20.38 Aligned_cols=14 Identities=21% Similarity=0.347 Sum_probs=9.4
Q ss_pred ceeecccccccccc
Q psy4404 2 ILVICQYCEVRLES 15 (151)
Q Consensus 2 ~~~~C~~C~~~f~~ 15 (151)
.+.+||.||..-..
T Consensus 2 ~LkPCPFCG~~~~~ 15 (61)
T PF14354_consen 2 ELKPCPFCGSADVL 15 (61)
T ss_pred CCcCCCCCCCcceE
Confidence 46778888866433
No 172
>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=44.55 E-value=12 Score=17.21 Aligned_cols=11 Identities=27% Similarity=0.588 Sum_probs=4.8
Q ss_pred eeecccccccc
Q psy4404 3 LVICQYCEVRL 13 (151)
Q Consensus 3 ~~~C~~C~~~f 13 (151)
.|+|+.|+..+
T Consensus 13 kY~Cp~C~~~~ 23 (30)
T PF04438_consen 13 KYRCPRCGARY 23 (30)
T ss_dssp SEE-TTT--EE
T ss_pred EEECCCcCCce
Confidence 36677776654
No 173
>KOG0717|consensus
Probab=44.17 E-value=11 Score=29.31 Aligned_cols=23 Identities=22% Similarity=0.543 Sum_probs=19.4
Q ss_pred eeCCcCCccccCHHHHHHHHhhh
Q psy4404 97 FKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
-.|..|+..|-++..|-.|++.-
T Consensus 461 ~~C~tCr~~FdSRnkLF~Hlk~t 483 (508)
T KOG0717|consen 461 ISCTTCRESFDSRNKLFAHLKKT 483 (508)
T ss_pred HhhhhhhhhccchhHHHHHhhhc
Confidence 46888999999999999998753
No 174
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=44.13 E-value=11 Score=17.38 Aligned_cols=9 Identities=33% Similarity=0.969 Sum_probs=5.8
Q ss_pred eeecccccc
Q psy4404 3 LVICQYCEV 11 (151)
Q Consensus 3 ~~~C~~C~~ 11 (151)
+|+|+.|+-
T Consensus 19 ~~vCp~C~~ 27 (30)
T PF08274_consen 19 LLVCPECGH 27 (30)
T ss_dssp SEEETTTTE
T ss_pred EEeCCcccc
Confidence 567777764
No 175
>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=44.04 E-value=11 Score=17.97 Aligned_cols=13 Identities=15% Similarity=0.391 Sum_probs=6.0
Q ss_pred eccccccccccCc
Q psy4404 5 ICQYCEVRLESNS 17 (151)
Q Consensus 5 ~C~~C~~~f~~~~ 17 (151)
.|.+||+.|....
T Consensus 5 ~C~eC~~~f~dSy 17 (34)
T PF01286_consen 5 KCDECGKPFMDSY 17 (34)
T ss_dssp E-TTT--EES-SS
T ss_pred hHhHhCCHHHHHH
Confidence 5788888886633
No 176
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=43.97 E-value=19 Score=21.93 Aligned_cols=15 Identities=33% Similarity=0.587 Sum_probs=10.6
Q ss_pred ceeeccccccccccC
Q psy4404 2 ILVICQYCEVRLESN 16 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~ 16 (151)
|+.+|+.||..-.-.
T Consensus 1 ~p~~CpYCg~~~~l~ 15 (102)
T PF11672_consen 1 KPIICPYCGGPAELV 15 (102)
T ss_pred CCcccCCCCCeeEEc
Confidence 567899998874433
No 177
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=43.69 E-value=95 Score=20.58 Aligned_cols=57 Identities=21% Similarity=0.464 Sum_probs=35.6
Q ss_pred eeCcccccccCChHHHHHHHhhhCCCCceeCCc--CCccccCHHHHHHHHhhhc-CCccccc
Q psy4404 69 FHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTI--CSHKAARKDHMKRHLQLKH-NADLSSM 127 (151)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~--C~~~f~~~~~l~~H~~~~~-~~~~~~~ 127 (151)
..||.|.......... .-.+.+...|+-.|.. |... -....|+.|.+..| ..+|-+.
T Consensus 81 L~CPLCRG~V~GWtvv-e~AR~~LN~K~RsC~~e~C~F~-GtY~eLrKHar~~HP~~rP~~v 140 (162)
T PF07800_consen 81 LACPLCRGEVKGWTVV-EPARRFLNAKKRSCSQESCSFS-GTYSELRKHARSEHPSARPSEV 140 (162)
T ss_pred ccCccccCceeceEEc-hHHHHHhccCCccCcccccccc-cCHHHHHHHHHhhCCCCCCccC
Confidence 5788887655544433 3356666777777765 5432 35678999998765 4444443
No 178
>KOG1842|consensus
Probab=42.55 E-value=9.4 Score=29.45 Aligned_cols=22 Identities=27% Similarity=0.546 Sum_probs=19.6
Q ss_pred eeccccccccccCchHHHHHHhh
Q psy4404 4 VICQYCEVRLESNSKELLEHCKT 26 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~ 26 (151)
|.||.|.+.|.+.. .|..|...
T Consensus 16 flCPiC~~dl~~~~-~L~~H~d~ 37 (505)
T KOG1842|consen 16 FLCPICLLDLPNLS-ALNDHLDV 37 (505)
T ss_pred ccCchHhhhhhhHH-HHHHHHhh
Confidence 78999999999999 99999643
No 179
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=42.35 E-value=23 Score=18.19 Aligned_cols=14 Identities=14% Similarity=0.451 Sum_probs=7.4
Q ss_pred eeccccccccccCc
Q psy4404 4 VICQYCEVRLESNS 17 (151)
Q Consensus 4 ~~C~~C~~~f~~~~ 17 (151)
|.|..||-++.-..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 55666665554433
No 180
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=41.81 E-value=13 Score=27.30 Aligned_cols=48 Identities=17% Similarity=0.302 Sum_probs=30.0
Q ss_pred eCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHHHHHhhh
Q psy4404 70 HCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKRHLQLK 119 (151)
Q Consensus 70 ~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H~~~~ 119 (151)
.|-.|...|+-...-.--. -+....|.|+.|...|...-+.-.|-..|
T Consensus 364 ~Cf~CQ~~fp~~~~~~~~~--~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh 411 (421)
T COG5151 364 HCFVCQGPFPKPPVSPFDE--STSSGRYQCELCKSTFCSDCDVFIHETLH 411 (421)
T ss_pred cceeccCCCCCCCCCcccc--cccccceechhhhhhhhhhhHHHHHHHHh
Confidence 3666766665543211111 12234699999999998888877777665
No 181
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=41.49 E-value=17 Score=28.03 Aligned_cols=15 Identities=20% Similarity=0.596 Sum_probs=9.5
Q ss_pred ceeeccCCCCcccCCch
Q psy4404 38 KYVCLYQKCSYHTGNSD 54 (151)
Q Consensus 38 ~~~C~~~~C~~~f~~~~ 54 (151)
.|+| +.||..+....
T Consensus 367 g~rC--~kCg~~~~~~~ 381 (421)
T COG1571 367 GFRC--KKCGTRARETL 381 (421)
T ss_pred Cccc--ccccccCCccc
Confidence 4677 66777666544
No 182
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=41.42 E-value=5.4 Score=32.57 Aligned_cols=58 Identities=21% Similarity=0.388 Sum_probs=0.0
Q ss_pred eee-ccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccc
Q psy4404 3 LVI-CQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCE 75 (151)
Q Consensus 3 ~~~-C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~ 75 (151)
||+ |..||=.|.-.. .|=.= ....+....-.| +.|.+-|.+..+-+-|. .|..|+.||
T Consensus 122 PF~~CT~CGPRfTIi~-alPYD------R~nTsM~~F~lC--~~C~~EY~dP~nRRfHA------Qp~aCp~CG 180 (750)
T COG0068 122 PFINCTNCGPRFTIIE-ALPYD------RENTSMADFPLC--PFCDKEYKDPLNRRFHA------QPIACPKCG 180 (750)
T ss_pred cccccCCCCcceeeec-cCCCC------cccCccccCcCC--HHHHHHhcCcccccccc------ccccCcccC
No 183
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=40.97 E-value=11 Score=26.36 Aligned_cols=16 Identities=19% Similarity=0.316 Sum_probs=11.9
Q ss_pred ceeeccccccccccCc
Q psy4404 2 ILVICQYCEVRLESNS 17 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~ 17 (151)
++.+|++||..|+-..
T Consensus 180 kpqRCpECGqVFKLVr 195 (268)
T PTZ00043 180 FLYRCGECDQIFMLVR 195 (268)
T ss_pred CCccCCCCCcEEEEEE
Confidence 4678999999986544
No 184
>PLN03239 histone acetyltransferase; Provisional
Probab=40.66 E-value=34 Score=25.69 Aligned_cols=39 Identities=26% Similarity=0.395 Sum_probs=28.8
Q ss_pred ceeeccccccccccCchHHHHHHhh--cCCCCCCCCCcceee
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKT--CKNLSRPDVSFKYVC 41 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~--~~~~~~~~~~~~~~C 41 (151)
.+|+|..|=+-|.+.. .|..|+.. +-..+.+.|...|+.
T Consensus 105 ~lYiCE~Clky~~~~~-~l~~H~~~~~~c~~~~PPG~eIYR~ 145 (351)
T PLN03239 105 VLYVCEFSFGFFARKS-ELLRFQAKELPKERRHPPGNEIYRC 145 (351)
T ss_pred eEEEeccchhhhcCHH-HHHHHHHhhccccCcCCCCCeEEEe
Confidence 5899999999998888 99999643 123444567777776
No 185
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=40.25 E-value=13 Score=19.80 Aligned_cols=13 Identities=15% Similarity=0.626 Sum_probs=7.7
Q ss_pred eccccccccccCc
Q psy4404 5 ICQYCEVRLESNS 17 (151)
Q Consensus 5 ~C~~C~~~f~~~~ 17 (151)
+|+.||+.|....
T Consensus 7 ~C~~Cg~~~~~~d 19 (54)
T PF14446_consen 7 KCPVCGKKFKDGD 19 (54)
T ss_pred cChhhCCcccCCC
Confidence 4666666665433
No 186
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=40.05 E-value=18 Score=26.72 Aligned_cols=10 Identities=30% Similarity=0.597 Sum_probs=6.4
Q ss_pred CceeCCcCCc
Q psy4404 95 KPFKCTICSH 104 (151)
Q Consensus 95 ~~~~C~~C~~ 104 (151)
+...|..|+.
T Consensus 251 r~e~C~~C~~ 260 (309)
T PRK03564 251 KAESCGDCGT 260 (309)
T ss_pred Eeeecccccc
Confidence 4467777764
No 187
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=39.93 E-value=20 Score=17.52 Aligned_cols=13 Identities=8% Similarity=0.092 Sum_probs=5.6
Q ss_pred CCCCcccCCchHH
Q psy4404 44 QKCSYHTGNSDHM 56 (151)
Q Consensus 44 ~~C~~~f~~~~~l 56 (151)
+.|+-.|.+...|
T Consensus 23 ~~C~G~W~d~~el 35 (41)
T PF13453_consen 23 PSCGGIWFDAGEL 35 (41)
T ss_pred CCCCeEEccHHHH
Confidence 4444444444433
No 188
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=39.85 E-value=13 Score=19.98 Aligned_cols=11 Identities=45% Similarity=1.135 Sum_probs=5.5
Q ss_pred CCCceeCcccc
Q psy4404 65 GEKAFHCPHCE 75 (151)
Q Consensus 65 ~~~~~~C~~C~ 75 (151)
|+....|+-|.
T Consensus 41 GE~VArCPSCS 51 (67)
T COG5216 41 GEVVARCPSCS 51 (67)
T ss_pred CceEEEcCCce
Confidence 44445555553
No 189
>KOG2593|consensus
Probab=39.63 E-value=36 Score=26.25 Aligned_cols=38 Identities=24% Similarity=0.558 Sum_probs=26.3
Q ss_pred cCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCc
Q psy4404 64 TGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSH 104 (151)
Q Consensus 64 ~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 104 (151)
.....|.|+.|.+.|.....+. ......-.|.|..|+.
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~~---L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEALQ---LLDNETGEFHCENCGG 161 (436)
T ss_pred cccccccCCccccchhhhHHHH---hhcccCceEEEecCCC
Confidence 3456699999999998766543 2233233689999986
No 190
>KOG2272|consensus
Probab=38.93 E-value=13 Score=26.50 Aligned_cols=13 Identities=23% Similarity=0.605 Sum_probs=10.3
Q ss_pred CceeCCcCCcccc
Q psy4404 95 KPFKCTICSHKAA 107 (151)
Q Consensus 95 ~~~~C~~C~~~f~ 107 (151)
..|.|..|.+.|.
T Consensus 220 eHFvCa~CekPFl 232 (332)
T KOG2272|consen 220 EHFVCAKCEKPFL 232 (332)
T ss_pred hheeehhcCCccc
Confidence 4688999998875
No 191
>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=38.38 E-value=5.1 Score=29.06 Aligned_cols=35 Identities=14% Similarity=0.456 Sum_probs=11.8
Q ss_pred eeCcccccccCChHHHHHHHhhhCCCCceeCCcCCc
Q psy4404 69 FHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSH 104 (151)
Q Consensus 69 ~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~ 104 (151)
..|+.|+..-...-.+.. .....+.+.+.|..|+.
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~-~e~~~~~rve~C~~C~~ 246 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFT-VEGEPAYRVEVCESCGS 246 (290)
T ss_dssp TS-TTT---SS-EEE---------SEEEEEETTTTE
T ss_pred CCCcCCCCCCCcceeeEe-cCCCCcEEEEECCcccc
Confidence 357777665433322210 11122334466777764
No 192
>PTZ00448 hypothetical protein; Provisional
Probab=38.23 E-value=17 Score=27.38 Aligned_cols=19 Identities=21% Similarity=0.558 Sum_probs=8.6
Q ss_pred CCCCcccCCchHHHHHHHh
Q psy4404 44 QKCSYHTGNSDHMRRHIRR 62 (151)
Q Consensus 44 ~~C~~~f~~~~~l~~h~~~ 62 (151)
..|+..|.+....+.|+++
T Consensus 318 ~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 318 RKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred cccccccCCHHHHHHHhhh
Confidence 4444444444444444443
No 193
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=37.97 E-value=62 Score=17.24 Aligned_cols=9 Identities=22% Similarity=0.442 Sum_probs=3.7
Q ss_pred CCCCcccCC
Q psy4404 44 QKCSYHTGN 52 (151)
Q Consensus 44 ~~C~~~f~~ 52 (151)
..|+-.|..
T Consensus 28 ~~C~H~fek 36 (57)
T PF11789_consen 28 KKCGHTFEK 36 (57)
T ss_dssp SSS--EEEH
T ss_pred CCCCCeecH
Confidence 456655554
No 194
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=37.80 E-value=15 Score=20.15 Aligned_cols=10 Identities=30% Similarity=0.664 Sum_probs=6.2
Q ss_pred eecccccccc
Q psy4404 4 VICQYCEVRL 13 (151)
Q Consensus 4 ~~C~~C~~~f 13 (151)
.+||.|++..
T Consensus 7 v~CP~C~k~~ 16 (62)
T PRK00418 7 VNCPTCGKPV 16 (62)
T ss_pred ccCCCCCCcc
Confidence 4566666654
No 195
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=37.63 E-value=22 Score=18.47 Aligned_cols=12 Identities=17% Similarity=0.523 Sum_probs=6.4
Q ss_pred eecccccccccc
Q psy4404 4 VICQYCEVRLES 15 (151)
Q Consensus 4 ~~C~~C~~~f~~ 15 (151)
|+|..||-++.-
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 455556555543
No 196
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.15 E-value=22 Score=29.48 Aligned_cols=11 Identities=27% Similarity=0.730 Sum_probs=6.0
Q ss_pred CceeCcccccc
Q psy4404 67 KAFHCPHCEYR 77 (151)
Q Consensus 67 ~~~~C~~C~~~ 77 (151)
.|..|+.|+..
T Consensus 474 ~p~~Cp~Cgs~ 484 (730)
T COG1198 474 IPQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCCC
Confidence 44556666554
No 197
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.83 E-value=10 Score=19.50 Aligned_cols=12 Identities=25% Similarity=0.658 Sum_probs=6.5
Q ss_pred eccccccccccC
Q psy4404 5 ICQYCEVRLESN 16 (151)
Q Consensus 5 ~C~~C~~~f~~~ 16 (151)
+|+.|++-|.-+
T Consensus 14 ICpvCqRPFsWR 25 (54)
T COG4338 14 ICPVCQRPFSWR 25 (54)
T ss_pred hhhhhcCchHHH
Confidence 356666655443
No 198
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=36.51 E-value=21 Score=22.51 Aligned_cols=13 Identities=23% Similarity=0.521 Sum_probs=11.1
Q ss_pred ceeeccccccccc
Q psy4404 2 ILVICQYCEVRLE 14 (151)
Q Consensus 2 ~~~~C~~C~~~f~ 14 (151)
+.|+|+.||..+.
T Consensus 6 ~fYkC~~CGniv~ 18 (125)
T TIGR00320 6 QVYKCEVCGNIVE 18 (125)
T ss_pred cEEECCCCCcEEE
Confidence 4899999999884
No 199
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=36.46 E-value=14 Score=16.15 Aligned_cols=7 Identities=29% Similarity=1.032 Sum_probs=3.2
Q ss_pred ecccccc
Q psy4404 5 ICQYCEV 11 (151)
Q Consensus 5 ~C~~C~~ 11 (151)
.|+.||.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 3444444
No 200
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.44 E-value=27 Score=22.12 Aligned_cols=14 Identities=21% Similarity=0.560 Sum_probs=7.5
Q ss_pred cceeeccCCCCcccCC
Q psy4404 37 FKYVCLYQKCSYHTGN 52 (151)
Q Consensus 37 ~~~~C~~~~C~~~f~~ 52 (151)
..|.| ..|++.|..
T Consensus 52 qRyrC--~~C~~tf~~ 65 (129)
T COG3677 52 QRYKC--KSCGSTFTV 65 (129)
T ss_pred ccccc--CCcCcceee
Confidence 34555 556555544
No 201
>KOG0717|consensus
Probab=36.41 E-value=17 Score=28.32 Aligned_cols=24 Identities=25% Similarity=0.587 Sum_probs=16.4
Q ss_pred eeccccccccccCchHHHHHHhhcC
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCK 28 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~ 28 (151)
..|..|+.+|.++. -|..|++.-+
T Consensus 461 ~~C~tCr~~FdSRn-kLF~Hlk~tg 484 (508)
T KOG0717|consen 461 ISCTTCRESFDSRN-KLFAHLKKTG 484 (508)
T ss_pred Hhhhhhhhhccchh-HHHHHhhhcC
Confidence 45777777777777 7777764433
No 202
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=36.40 E-value=33 Score=25.78 Aligned_cols=29 Identities=31% Similarity=0.613 Sum_probs=24.4
Q ss_pred CceeeccccccccccCchHHHHHHhhcCCC
Q psy4404 1 MILVICQYCEVRLESNSKELLEHCKTCKNL 30 (151)
Q Consensus 1 ~~~~~C~~C~~~f~~~~~~l~~H~~~~~~~ 30 (151)
.++|+|..|=+-|.+.. .|+.|.+.|.=.
T Consensus 156 d~vyICefClkY~~s~~-~~~rH~~kC~~~ 184 (395)
T COG5027 156 DIVYICEFCLKYYGSQT-SLVRHRKKCSLQ 184 (395)
T ss_pred ceEEEhhhhHHHhcchh-HHHHHHhcCcCc
Confidence 36899999999999999 999997766533
No 203
>COG1773 Rubredoxin [Energy production and conversion]
Probab=36.17 E-value=20 Score=19.11 Aligned_cols=17 Identities=18% Similarity=0.341 Sum_probs=9.1
Q ss_pred CceeeccccccccccCc
Q psy4404 1 MILVICQYCEVRLESNS 17 (151)
Q Consensus 1 ~~~~~C~~C~~~f~~~~ 17 (151)
|+.|.|..||-+|.-..
T Consensus 1 m~~~~C~~CG~vYd~e~ 17 (55)
T COG1773 1 MKRWRCSVCGYVYDPEK 17 (55)
T ss_pred CCceEecCCceEecccc
Confidence 34556666666654433
No 204
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=35.76 E-value=20 Score=27.99 Aligned_cols=21 Identities=24% Similarity=0.604 Sum_probs=18.8
Q ss_pred eccccccccccCchHHHHHHhh
Q psy4404 5 ICQYCEVRLESNSKELLEHCKT 26 (151)
Q Consensus 5 ~C~~C~~~f~~~~~~l~~H~~~ 26 (151)
.|+.|+++|.... .+..|+..
T Consensus 59 iCp~CskkF~d~~-~~~~H~~~ 79 (466)
T PF04780_consen 59 ICPRCSKKFSDAE-SCLSHMEQ 79 (466)
T ss_pred eCCcccceeCCHH-HHHHHHHH
Confidence 6999999999998 99999764
No 205
>PF15616 TerY-C: TerY-C metal binding domain
Probab=34.16 E-value=22 Score=22.71 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=7.1
Q ss_pred ceeCccccccc
Q psy4404 68 AFHCPHCEYRC 78 (151)
Q Consensus 68 ~~~C~~C~~~~ 78 (151)
...||.|++.-
T Consensus 105 ~~~CPwCg~~g 115 (131)
T PF15616_consen 105 EVTCPWCGNEG 115 (131)
T ss_pred CEECCCCCCee
Confidence 46777777653
No 206
>PRK01343 zinc-binding protein; Provisional
Probab=34.02 E-value=19 Score=19.37 Aligned_cols=11 Identities=18% Similarity=0.302 Sum_probs=6.9
Q ss_pred eeccccccccc
Q psy4404 4 VICQYCEVRLE 14 (151)
Q Consensus 4 ~~C~~C~~~f~ 14 (151)
.+|+.|++.|.
T Consensus 10 ~~CP~C~k~~~ 20 (57)
T PRK01343 10 RPCPECGKPST 20 (57)
T ss_pred CcCCCCCCcCc
Confidence 35777777653
No 207
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=33.82 E-value=17 Score=19.16 Aligned_cols=11 Identities=36% Similarity=0.899 Sum_probs=6.8
Q ss_pred ecccccccccc
Q psy4404 5 ICQYCEVRLES 15 (151)
Q Consensus 5 ~C~~C~~~f~~ 15 (151)
.||.||..+..
T Consensus 2 ~CPyCge~~~~ 12 (52)
T PF14255_consen 2 QCPYCGEPIEI 12 (52)
T ss_pred CCCCCCCeeEE
Confidence 46777766543
No 208
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=33.59 E-value=20 Score=17.56 Aligned_cols=12 Identities=17% Similarity=0.595 Sum_probs=8.0
Q ss_pred eecccccccccc
Q psy4404 4 VICQYCEVRLES 15 (151)
Q Consensus 4 ~~C~~C~~~f~~ 15 (151)
+.|+.||..+.+
T Consensus 33 ~~C~~CGE~~~~ 44 (46)
T TIGR03831 33 LVCPQCGEEYLD 44 (46)
T ss_pred cccccCCCEeeC
Confidence 358888877644
No 209
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=33.43 E-value=19 Score=17.31 Aligned_cols=11 Identities=18% Similarity=0.588 Sum_probs=5.5
Q ss_pred ecccccccccc
Q psy4404 5 ICQYCEVRLES 15 (151)
Q Consensus 5 ~C~~C~~~f~~ 15 (151)
.|+.|++.|--
T Consensus 4 ~CprC~kg~Hw 14 (36)
T PF14787_consen 4 LCPRCGKGFHW 14 (36)
T ss_dssp C-TTTSSSCS-
T ss_pred cCcccCCCcch
Confidence 36667666543
No 210
>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=33.13 E-value=21 Score=21.20 Aligned_cols=10 Identities=20% Similarity=0.713 Sum_probs=5.7
Q ss_pred eeeccccccc
Q psy4404 3 LVICQYCEVR 12 (151)
Q Consensus 3 ~~~C~~C~~~ 12 (151)
.|.||.||+.
T Consensus 35 ky~Cp~Cgk~ 44 (90)
T PF01780_consen 35 KYTCPFCGKT 44 (90)
T ss_dssp -BEESSSSSS
T ss_pred CCcCCCCCCc
Confidence 3566666665
No 211
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=32.92 E-value=18 Score=23.75 Aligned_cols=27 Identities=15% Similarity=0.198 Sum_probs=19.5
Q ss_pred CCCCceeCCcCCccccCHHHHHHHHhh
Q psy4404 92 TGEKPFKCTICSHKAARKDHMKRHLQL 118 (151)
Q Consensus 92 ~~~~~~~C~~C~~~f~~~~~l~~H~~~ 118 (151)
+.+.|..|..||+.|.|......-.+.
T Consensus 64 ~~~~PsYC~~CGkpyPWt~~~L~aa~e 90 (158)
T PF10083_consen 64 HYEAPSYCHNCGKPYPWTENALEAANE 90 (158)
T ss_pred CCCCChhHHhCCCCCchHHHHHHHHHH
Confidence 335788999999999987665554443
No 212
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=32.71 E-value=17 Score=19.78 Aligned_cols=16 Identities=25% Similarity=0.357 Sum_probs=9.8
Q ss_pred ceeeccccccccccCc
Q psy4404 2 ILVICQYCEVRLESNS 17 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~ 17 (151)
.|..|..||+...+.-
T Consensus 3 iPVRCFTCGkvi~~~~ 18 (60)
T PF01194_consen 3 IPVRCFTCGKVIGNKW 18 (60)
T ss_dssp -SSS-STTTSBTCGHH
T ss_pred CceecCCCCCChhHhH
Confidence 4566888888776654
No 213
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=32.08 E-value=32 Score=21.10 Aligned_cols=30 Identities=17% Similarity=0.571 Sum_probs=19.1
Q ss_pred eccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCch
Q psy4404 5 ICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSD 54 (151)
Q Consensus 5 ~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~ 54 (151)
.||.|+..|.+.. ..-|.| ++|+.-|....
T Consensus 4 ~CP~C~seytY~d------------------g~~~iC--peC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTYHD------------------GTQLIC--PSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceEec------------------CCeeEC--ccccccccccc
Confidence 4777776665543 223778 88887776543
No 214
>KOG1280|consensus
Probab=31.95 E-value=47 Score=24.96 Aligned_cols=21 Identities=19% Similarity=0.441 Sum_probs=13.0
Q ss_pred eeeccccccccccCchHHHHHH
Q psy4404 3 LVICQYCEVRLESNSKELLEHC 24 (151)
Q Consensus 3 ~~~C~~C~~~f~~~~~~l~~H~ 24 (151)
.|.||.|+++=.+.. .|+.|+
T Consensus 79 SftCPyC~~~Gfte~-~f~~Hv 99 (381)
T KOG1280|consen 79 SFTCPYCGIMGFTER-QFGTHV 99 (381)
T ss_pred cccCCcccccccchh-HHHHHh
Confidence 466666666655555 666665
No 215
>PRK10220 hypothetical protein; Provisional
Probab=31.90 E-value=39 Score=20.77 Aligned_cols=33 Identities=18% Similarity=0.506 Sum_probs=21.7
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCch
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSD 54 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~ 54 (151)
.+=.||.|+..|.+.. ..-|.| +.|+.-|....
T Consensus 2 ~lP~CP~C~seytY~d------------------~~~~vC--peC~hEW~~~~ 34 (111)
T PRK10220 2 SLPHCPKCNSEYTYED------------------NGMYIC--PECAHEWNDAE 34 (111)
T ss_pred CCCcCCCCCCcceEcC------------------CCeEEC--CcccCcCCccc
Confidence 3445888887776544 123888 88888777654
No 216
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=31.62 E-value=22 Score=18.95 Aligned_cols=10 Identities=30% Similarity=0.966 Sum_probs=7.7
Q ss_pred cccccccccc
Q psy4404 6 CQYCEVRLES 15 (151)
Q Consensus 6 C~~C~~~f~~ 15 (151)
||.||+.|..
T Consensus 42 CPfC~~~~~~ 51 (55)
T PF14447_consen 42 CPFCGTPFEF 51 (55)
T ss_pred CCCCCCcccC
Confidence 8888888754
No 217
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=31.46 E-value=34 Score=16.59 Aligned_cols=12 Identities=33% Similarity=0.744 Sum_probs=3.3
Q ss_pred ceeecccccccc
Q psy4404 2 ILVICQYCEVRL 13 (151)
Q Consensus 2 ~~~~C~~C~~~f 13 (151)
+-|-|+.|+..|
T Consensus 2 ~ryyCdyC~~~~ 13 (38)
T PF06220_consen 2 PRYYCDYCKKYL 13 (38)
T ss_dssp -S-B-TTT--B-
T ss_pred cCeeccccccee
Confidence 345555555555
No 218
>KOG4124|consensus
Probab=31.30 E-value=6.3 Score=29.37 Aligned_cols=71 Identities=21% Similarity=0.408 Sum_probs=40.5
Q ss_pred CcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCChHHHHHHHhhhCCCCceeCCcCCccccCHHHHHHH
Q psy4404 36 SFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQQSALYNHLKRHTGEKPFKCTICSHKAARKDHMKRH 115 (151)
Q Consensus 36 ~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~~~~l~~h~~~h~~~~~~~C~~C~~~f~~~~~l~~H 115 (151)
.++|.|+++.|.+.+.....|..|...-+ |...... .+ .-..|+-.....|+|+|++|.+++.....|..|
T Consensus 347 ~~~~~~~vp~~~~~~~n~ng~~~~~~~~h------~s~i~~~--s~-~~~ph~~~~~~nk~~r~~i~~~~~k~~~~l~~~ 417 (442)
T KOG4124|consen 347 DKPYKCPVPNCDKAYKNQNGLKYHKLHGH------CSPITTP--TP-APIPHQGFVVENKPYRCEVCSKRYKNLNGLKYH 417 (442)
T ss_pred cCCCCCCCCcchhhcccCcceeeccccCc------CCCCCCC--CC-CCCCcceeeeccCcccChhhhhhhccCCCCCce
Confidence 34688888889998888877766643221 1111000 00 111233233446789999998877665555444
No 219
>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=31.22 E-value=39 Score=18.44 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=6.7
Q ss_pred CceeCCcCCccc
Q psy4404 95 KPFKCTICSHKA 106 (151)
Q Consensus 95 ~~~~C~~C~~~f 106 (151)
+.|.|+.||...
T Consensus 45 r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 45 RVFTCPNCGFEM 56 (69)
T ss_pred ceEEcCCCCCEE
Confidence 346666666543
No 220
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=30.95 E-value=72 Score=28.46 Aligned_cols=9 Identities=22% Similarity=0.597 Sum_probs=5.9
Q ss_pred eeccccccc
Q psy4404 4 VICQYCEVR 12 (151)
Q Consensus 4 ~~C~~C~~~ 12 (151)
++||.||..
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 567777764
No 221
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=30.85 E-value=46 Score=17.77 Aligned_cols=14 Identities=21% Similarity=0.572 Sum_probs=8.2
Q ss_pred CCCceeCCcCCccc
Q psy4404 93 GEKPFKCTICSHKA 106 (151)
Q Consensus 93 ~~~~~~C~~C~~~f 106 (151)
+...|.|+.||..+
T Consensus 11 ~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 11 AHVNFECPDCGIPT 24 (55)
T ss_pred cccCCcCCCCCCcC
Confidence 34456777777543
No 222
>KOG3497|consensus
Probab=30.77 E-value=26 Score=19.05 Aligned_cols=16 Identities=19% Similarity=0.343 Sum_probs=10.5
Q ss_pred ceeeccccccccccCc
Q psy4404 2 ILVICQYCEVRLESNS 17 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~ 17 (151)
.|..|..|||...++=
T Consensus 3 iPiRCFtCGKvig~KW 18 (69)
T KOG3497|consen 3 IPIRCFTCGKVIGDKW 18 (69)
T ss_pred eeeEeeeccccccccH
Confidence 3566777777766654
No 223
>KOG3507|consensus
Probab=30.35 E-value=29 Score=18.76 Aligned_cols=10 Identities=30% Similarity=0.836 Sum_probs=5.6
Q ss_pred ceeecccccc
Q psy4404 2 ILVICQYCEV 11 (151)
Q Consensus 2 ~~~~C~~C~~ 11 (151)
+.|+|..||.
T Consensus 19 miYiCgdC~~ 28 (62)
T KOG3507|consen 19 MIYICGDCGQ 28 (62)
T ss_pred EEEEeccccc
Confidence 4556666654
No 224
>PF08782 c-SKI_SMAD_bind: c-SKI Smad4 binding domain; InterPro: IPR014890 c-SKI is an oncoprotein that inhibits TGF-beta signalling through interaction with Smad proteins []. This protein binds to Smad4 [].; GO: 0005634 nucleus; PDB: 1MR1_C.
Probab=29.76 E-value=21 Score=21.45 Aligned_cols=18 Identities=22% Similarity=0.466 Sum_probs=7.7
Q ss_pred eeccccccccccCchHHHHH
Q psy4404 4 VICQYCEVRLESNSKELLEH 23 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H 23 (151)
+.|..|+..| +.. .+..|
T Consensus 29 I~C~~C~~~F-sP~-kFV~H 46 (96)
T PF08782_consen 29 IECLECRGMF-SPQ-KFVFH 46 (96)
T ss_dssp EEETTT--EE--HH-HHTT-
T ss_pred eEcccCCCEe-CCc-CEEEe
Confidence 4566666665 333 45555
No 225
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.51 E-value=23 Score=21.50 Aligned_cols=12 Identities=33% Similarity=0.642 Sum_probs=7.5
Q ss_pred eecccccccccc
Q psy4404 4 VICQYCEVRLES 15 (151)
Q Consensus 4 ~~C~~C~~~f~~ 15 (151)
..||.||.-|..
T Consensus 50 t~CP~Cg~~~e~ 61 (115)
T COG1885 50 TSCPKCGEPFES 61 (115)
T ss_pred ccCCCCCCccce
Confidence 457777766543
No 226
>KOG1280|consensus
Probab=29.51 E-value=76 Score=23.90 Aligned_cols=24 Identities=13% Similarity=0.344 Sum_probs=12.4
Q ss_pred CcceeeccCCCCcccCCchHHHHHHH
Q psy4404 36 SFKYVCLYQKCSYHTGNSDHMRRHIR 61 (151)
Q Consensus 36 ~~~~~C~~~~C~~~f~~~~~l~~h~~ 61 (151)
+..|.| +.|+..-.+...|..|..
T Consensus 77 ~qSftC--PyC~~~Gfte~~f~~Hv~ 100 (381)
T KOG1280|consen 77 PQSFTC--PYCGIMGFTERQFGTHVL 100 (381)
T ss_pred cccccC--CcccccccchhHHHHHhh
Confidence 334555 555555555555555543
No 227
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=29.32 E-value=36 Score=22.32 Aligned_cols=8 Identities=25% Similarity=1.090 Sum_probs=3.9
Q ss_pred ceeCCcCC
Q psy4404 96 PFKCTICS 103 (151)
Q Consensus 96 ~~~C~~C~ 103 (151)
.|.|..|+
T Consensus 140 ~YrC~~C~ 147 (156)
T COG3091 140 VYRCGKCG 147 (156)
T ss_pred eEEeccCC
Confidence 45555554
No 228
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=29.26 E-value=19 Score=15.31 Aligned_cols=6 Identities=33% Similarity=1.143 Sum_probs=2.9
Q ss_pred cccccc
Q psy4404 6 CQYCEV 11 (151)
Q Consensus 6 C~~C~~ 11 (151)
|+.||.
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 444544
No 229
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=29.04 E-value=19 Score=19.99 Aligned_cols=38 Identities=16% Similarity=0.258 Sum_probs=18.6
Q ss_pred ceeeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccC
Q psy4404 2 ILVICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTG 51 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~ 51 (151)
+.|.|..|+..-....+....| .|--.-+| +.|.....
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY~----------~GvViv~C--~gC~~~Hl 40 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAYH----------KGVVIVQC--PGCKNRHL 40 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHHH----------TSEEEEE---TTS--EEE
T ss_pred EEEEcCCCCCccceeeCHHHHh----------CCeEEEEC--CCCcceee
Confidence 4678888875532222122233 45555667 77876533
No 230
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=28.98 E-value=52 Score=25.83 Aligned_cols=24 Identities=25% Similarity=0.580 Sum_probs=18.2
Q ss_pred eeCCcCCccccCHHHHHHHHhhhc
Q psy4404 97 FKCTICSHKAARKDHMKRHLQLKH 120 (151)
Q Consensus 97 ~~C~~C~~~f~~~~~l~~H~~~~~ 120 (151)
|.|+.|.+.|.....+..|+...|
T Consensus 58 WiCp~CskkF~d~~~~~~H~~~eH 81 (466)
T PF04780_consen 58 WICPRCSKKFSDAESCLSHMEQEH 81 (466)
T ss_pred eeCCcccceeCCHHHHHHHHHHhh
Confidence 678888888888888888877544
No 231
>PF14369 zf-RING_3: zinc-finger
Probab=28.38 E-value=27 Score=16.62 Aligned_cols=10 Identities=20% Similarity=0.547 Sum_probs=7.5
Q ss_pred eccccccccc
Q psy4404 5 ICQYCEVRLE 14 (151)
Q Consensus 5 ~C~~C~~~f~ 14 (151)
.||.|+..|-
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 4888888774
No 232
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=28.19 E-value=34 Score=15.31 Aligned_cols=12 Identities=25% Similarity=0.658 Sum_probs=4.0
Q ss_pred ceeecccccccc
Q psy4404 2 ILVICQYCEVRL 13 (151)
Q Consensus 2 ~~~~C~~C~~~f 13 (151)
..|.|.+|+-.+
T Consensus 14 ~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 14 WFYRCSECDFDL 25 (30)
T ss_dssp -EEE-TTT----
T ss_pred ceEECccCCCcc
Confidence 456677766443
No 233
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=28.10 E-value=23 Score=19.49 Aligned_cols=9 Identities=22% Similarity=0.552 Sum_probs=5.7
Q ss_pred eeccccccc
Q psy4404 4 VICQYCEVR 12 (151)
Q Consensus 4 ~~C~~C~~~ 12 (151)
|+|+.||..
T Consensus 1 y~C~KCg~~ 9 (64)
T PF09855_consen 1 YKCPKCGNE 9 (64)
T ss_pred CCCCCCCCc
Confidence 467777664
No 234
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=28.00 E-value=22 Score=18.54 Aligned_cols=12 Identities=17% Similarity=0.545 Sum_probs=8.0
Q ss_pred eeeccCCCCcccCC
Q psy4404 39 YVCLYQKCSYHTGN 52 (151)
Q Consensus 39 ~~C~~~~C~~~f~~ 52 (151)
+.| ..|+.....
T Consensus 27 ~~C--~~Cga~~~~ 38 (53)
T TIGR03655 27 FEC--STCGASGPV 38 (53)
T ss_pred EEC--CCCCCCccc
Confidence 467 778776555
No 235
>PF11931 DUF3449: Domain of unknown function (DUF3449); InterPro: IPR024598 This presumed domain is functionally uncharacterised. It has two conserved sequence motifs: PIP and CEICG and contains a zinc-finger of the C2H2-type.; PDB: 4DGW_A.
Probab=27.63 E-value=20 Score=24.55 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=0.0
Q ss_pred ceeeccccccccccCchHHHHHH
Q psy4404 2 ILVICQYCEVRLESNSKELLEHC 24 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~~~l~~H~ 24 (151)
+.|+|.+||...=.-.+++..|+
T Consensus 100 ~ey~CEICGN~~Y~GrkaFekHF 122 (196)
T PF11931_consen 100 VEYKCEICGNQSYKGRKAFEKHF 122 (196)
T ss_dssp -----------------------
T ss_pred CeeeeEeCCCcceecHHHHHHhc
Confidence 45788888876433334777773
No 236
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=27.54 E-value=44 Score=21.55 Aligned_cols=46 Identities=20% Similarity=0.221 Sum_probs=27.4
Q ss_pred ceeeccCCCCcccCCchHHHHHHHhh-----cCCCceeCcccccccCChHHHH
Q psy4404 38 KYVCLYQKCSYHTGNSDHMRRHIRRH-----TGEKAFHCPHCEYRCSQQSALY 85 (151)
Q Consensus 38 ~~~C~~~~C~~~f~~~~~l~~h~~~h-----~~~~~~~C~~C~~~~~~~~~l~ 85 (151)
.-.| ..|+..+.....-..-..+. .....+.|+.|++.|..-+.+.
T Consensus 91 ~sRC--~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH~~ 141 (147)
T PF01927_consen 91 FSRC--PKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSHWR 141 (147)
T ss_pred CCcc--CCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccccHH
Confidence 4678 88988765543211111111 1234688999999998766554
No 237
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=27.47 E-value=21 Score=19.07 Aligned_cols=10 Identities=20% Similarity=0.703 Sum_probs=2.3
Q ss_pred eeeccccccc
Q psy4404 3 LVICQYCEVR 12 (151)
Q Consensus 3 ~~~C~~C~~~ 12 (151)
-|+|+.||.+
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 3556666654
No 238
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.05 E-value=76 Score=18.30 Aligned_cols=27 Identities=15% Similarity=0.158 Sum_probs=17.4
Q ss_pred CCCcceeeccCCCCcccCCchHHHHHHHh
Q psy4404 34 DVSFKYVCLYQKCSYHTGNSDHMRRHIRR 62 (151)
Q Consensus 34 ~~~~~~~C~~~~C~~~f~~~~~l~~h~~~ 62 (151)
.+...-.| +.|+-.+.+...|.+-+..
T Consensus 17 s~vEiD~C--PrCrGVWLDrGELdKli~r 43 (88)
T COG3809 17 SGVEIDYC--PRCRGVWLDRGELDKLIER 43 (88)
T ss_pred cCceeeeC--CccccEeecchhHHHHHHH
Confidence 34344557 7788888887777666543
No 239
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=26.91 E-value=82 Score=19.05 Aligned_cols=12 Identities=17% Similarity=0.495 Sum_probs=7.4
Q ss_pred eeCcccccccCC
Q psy4404 69 FHCPHCEYRCSQ 80 (151)
Q Consensus 69 ~~C~~C~~~~~~ 80 (151)
..|+.|+..+..
T Consensus 43 ~~C~~CG~y~~~ 54 (99)
T PRK14892 43 ITCGNCGLYTEF 54 (99)
T ss_pred EECCCCCCccCE
Confidence 567777765543
No 240
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=26.82 E-value=29 Score=15.53 Aligned_cols=11 Identities=27% Similarity=0.531 Sum_probs=3.9
Q ss_pred ecccccccccc
Q psy4404 5 ICQYCEVRLES 15 (151)
Q Consensus 5 ~C~~C~~~f~~ 15 (151)
+|+.|+..+..
T Consensus 3 ~C~rC~~~~~~ 13 (30)
T PF06827_consen 3 KCPRCWNYIED 13 (30)
T ss_dssp B-TTT--BBEE
T ss_pred cCccCCCcceE
Confidence 35555555433
No 241
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=26.63 E-value=26 Score=21.17 Aligned_cols=40 Identities=13% Similarity=0.358 Sum_probs=22.9
Q ss_pred CCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccCC
Q psy4404 35 VSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCSQ 80 (151)
Q Consensus 35 ~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~~ 80 (151)
-++.|.| +.|+..-...-.+..- .......|..|+..|..
T Consensus 19 L~k~FtC--p~Cghe~vs~ctvkk~----~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 19 LPKTFTC--PRCGHEKVSSCTVKKT----VNIGTAVCGNCGLSFEC 58 (104)
T ss_pred CCceEec--CccCCeeeeEEEEEec----CceeEEEcccCcceEEE
Confidence 3566888 7788765554333222 22334567777776644
No 242
>PF14375 Cys_rich_CWC: Cysteine-rich CWC
Probab=26.58 E-value=31 Score=17.76 Aligned_cols=6 Identities=17% Similarity=0.440 Sum_probs=2.2
Q ss_pred cccccc
Q psy4404 7 QYCEVR 12 (151)
Q Consensus 7 ~~C~~~ 12 (151)
|.||..
T Consensus 2 P~Cg~~ 7 (50)
T PF14375_consen 2 PRCGAP 7 (50)
T ss_pred CCCCCc
Confidence 333333
No 243
>KOG2636|consensus
Probab=26.54 E-value=61 Score=25.29 Aligned_cols=32 Identities=22% Similarity=0.406 Sum_probs=25.6
Q ss_pred HhhhCCCCceeCCcCC-ccccCHHHHHHHHhhh
Q psy4404 88 LKRHTGEKPFKCTICS-HKAARKDHMKRHLQLK 119 (151)
Q Consensus 88 ~~~h~~~~~~~C~~C~-~~f~~~~~l~~H~~~~ 119 (151)
.+.|.-...|.|.+|| ..+.-+..+.+|....
T Consensus 393 yKLHGL~~ey~CEICGNy~Y~GrkaF~RHF~Ew 425 (497)
T KOG2636|consen 393 YKLHGLDIEYNCEICGNYVYKGRKAFDRHFNEW 425 (497)
T ss_pred HhhcCCCcccceeeccCccccCcHHHHHHhHHH
Confidence 4667777789999999 7888888888887753
No 244
>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=26.04 E-value=16 Score=20.04 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=4.4
Q ss_pred eccccccccc
Q psy4404 5 ICQYCEVRLE 14 (151)
Q Consensus 5 ~C~~C~~~f~ 14 (151)
.|..|++.|.
T Consensus 11 ~C~~C~~~F~ 20 (69)
T PF01363_consen 11 NCMICGKKFS 20 (69)
T ss_dssp B-TTT--B-B
T ss_pred cCcCcCCcCC
Confidence 5888999983
No 245
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=26.00 E-value=37 Score=20.99 Aligned_cols=10 Identities=30% Similarity=0.979 Sum_probs=5.6
Q ss_pred eeCccccccc
Q psy4404 69 FHCPHCEYRC 78 (151)
Q Consensus 69 ~~C~~C~~~~ 78 (151)
|-|+.||...
T Consensus 75 yyCP~Cgt~l 84 (112)
T PF08882_consen 75 YYCPGCGTQL 84 (112)
T ss_pred EECCCCccee
Confidence 5566665443
No 246
>PRK08222 hydrogenase 4 subunit H; Validated
Probab=25.65 E-value=34 Score=23.01 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=6.7
Q ss_pred eeccccccccccC
Q psy4404 4 VICQYCEVRLESN 16 (151)
Q Consensus 4 ~~C~~C~~~f~~~ 16 (151)
+.|..||+.|...
T Consensus 115 ~~C~~Cg~~f~~~ 127 (181)
T PRK08222 115 QRCSRCERPFAPQ 127 (181)
T ss_pred CcCcccCCccCcH
Confidence 3455555555543
No 247
>KOG0978|consensus
Probab=25.37 E-value=12 Score=30.78 Aligned_cols=16 Identities=19% Similarity=0.561 Sum_probs=11.3
Q ss_pred eCcccccccCChHHHH
Q psy4404 70 HCPHCEYRCSQQSALY 85 (151)
Q Consensus 70 ~C~~C~~~~~~~~~l~ 85 (151)
.||.|+.+|.......
T Consensus 680 KCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 680 KCPKCNAAFGANDVHR 695 (698)
T ss_pred CCCCCCCCCCcccccc
Confidence 5888888887766543
No 248
>PRK12496 hypothetical protein; Provisional
Probab=25.27 E-value=55 Score=21.69 Aligned_cols=12 Identities=25% Similarity=0.576 Sum_probs=8.1
Q ss_pred eeeccCCCCcccCC
Q psy4404 39 YVCLYQKCSYHTGN 52 (151)
Q Consensus 39 ~~C~~~~C~~~f~~ 52 (151)
|.| .+|++.|..
T Consensus 128 ~~C--~gC~~~~~~ 139 (164)
T PRK12496 128 KVC--KGCKKKYPE 139 (164)
T ss_pred EEC--CCCCccccC
Confidence 667 777777653
No 249
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.04 E-value=32 Score=24.26 Aligned_cols=16 Identities=13% Similarity=0.557 Sum_probs=13.5
Q ss_pred ceeeccccccccccCc
Q psy4404 2 ILVICQYCEVRLESNS 17 (151)
Q Consensus 2 ~~~~C~~C~~~f~~~~ 17 (151)
+-+.||+|+.+|..+.
T Consensus 18 k~ieCPvC~tkFkkee 33 (267)
T COG1655 18 KTIECPVCNTKFKKEE 33 (267)
T ss_pred ceeccCcccchhhhhh
Confidence 4578999999998877
No 250
>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=24.88 E-value=33 Score=20.39 Aligned_cols=14 Identities=21% Similarity=0.524 Sum_probs=8.9
Q ss_pred cceeeccCCCCcccCC
Q psy4404 37 FKYVCLYQKCSYHTGN 52 (151)
Q Consensus 37 ~~~~C~~~~C~~~f~~ 52 (151)
-.+.| ..|++.|.-
T Consensus 52 GIW~C--~~C~~~~AG 65 (91)
T TIGR00280 52 GIWTC--RKCGAKFAG 65 (91)
T ss_pred EEEEc--CCCCCEEeC
Confidence 35677 777776544
No 251
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=24.81 E-value=37 Score=17.52 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=9.4
Q ss_pred eeecccccccccc
Q psy4404 3 LVICQYCEVRLES 15 (151)
Q Consensus 3 ~~~C~~C~~~f~~ 15 (151)
+..|..||..+..
T Consensus 5 ~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 5 LLRCGHCGSKMTR 17 (58)
T ss_pred cEEcccCCcEeEE
Confidence 4678888877655
No 252
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=24.70 E-value=43 Score=20.72 Aligned_cols=12 Identities=25% Similarity=0.617 Sum_probs=5.9
Q ss_pred eeeccCCCCcccCC
Q psy4404 39 YVCLYQKCSYHTGN 52 (151)
Q Consensus 39 ~~C~~~~C~~~f~~ 52 (151)
..| ..|+..|..
T Consensus 71 ~~C--~~Cg~~~~~ 82 (115)
T TIGR00100 71 CEC--EDCSEEVSP 82 (115)
T ss_pred EEc--ccCCCEEec
Confidence 445 555544443
No 253
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=24.69 E-value=36 Score=18.65 Aligned_cols=17 Identities=29% Similarity=0.423 Sum_probs=11.9
Q ss_pred CceeeccccccccccCc
Q psy4404 1 MILVICQYCEVRLESNS 17 (151)
Q Consensus 1 ~~~~~C~~C~~~f~~~~ 17 (151)
+.|..|..||+...+.-
T Consensus 2 iiPvRCFTCGkvi~~~w 18 (62)
T PRK04016 2 MIPVRCFTCGKVIAEKW 18 (62)
T ss_pred CCCeEecCCCCChHHHH
Confidence 35677888888876644
No 254
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=24.45 E-value=32 Score=17.37 Aligned_cols=8 Identities=25% Similarity=0.667 Sum_probs=4.2
Q ss_pred eccccccc
Q psy4404 5 ICQYCEVR 12 (151)
Q Consensus 5 ~C~~C~~~ 12 (151)
+||.||..
T Consensus 13 kCp~CGt~ 20 (44)
T PF14952_consen 13 KCPKCGTY 20 (44)
T ss_pred cCCcCcCc
Confidence 45555543
No 255
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=24.31 E-value=43 Score=26.94 Aligned_cols=43 Identities=23% Similarity=0.369 Sum_probs=25.4
Q ss_pred eeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCcccCCch
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSYHTGNSD 54 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~~f~~~~ 54 (151)
.+||+||..+.-.-.. ++...+. ....-.|.| +.||..+....
T Consensus 201 vpCPhCg~~~~l~~~~----l~w~~~~--~~~~a~y~C--~~Cg~~i~e~~ 243 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWEN----LKWDKGE--APETARYVC--PHCGCEIEEHD 243 (557)
T ss_pred ccCCCCCCCccccccc----eeecCCC--CccceEEEC--CCCcCCCCHHH
Confidence 4699999988654312 2221111 223345889 88998877644
No 256
>KOG1729|consensus
Probab=24.21 E-value=47 Score=24.28 Aligned_cols=24 Identities=29% Similarity=0.582 Sum_probs=16.6
Q ss_pred eeccccccccccCchHHHHHHhhcC
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCK 28 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~ 28 (151)
-.|..|++.+.+.. .-..|++.|+
T Consensus 169 ~~C~~C~~~~Ftl~-~RRHHCR~CG 192 (288)
T KOG1729|consen 169 TECMVCGCTEFTLS-ERRHHCRNCG 192 (288)
T ss_pred eecccCCCccccHH-HHHHHHHhcc
Confidence 36999999766666 6667755444
No 257
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=23.98 E-value=32 Score=16.50 Aligned_cols=12 Identities=25% Similarity=0.379 Sum_probs=7.9
Q ss_pred eecccccccccc
Q psy4404 4 VICQYCEVRLES 15 (151)
Q Consensus 4 ~~C~~C~~~f~~ 15 (151)
++|++|+..+..
T Consensus 9 ~~C~~C~~~~~~ 20 (36)
T PF11781_consen 9 EPCPVCGSRWFY 20 (36)
T ss_pred CcCCCCCCeEeE
Confidence 358888887433
No 258
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.79 E-value=56 Score=20.15 Aligned_cols=12 Identities=25% Similarity=0.304 Sum_probs=6.3
Q ss_pred eeeccCCCCcccCC
Q psy4404 39 YVCLYQKCSYHTGN 52 (151)
Q Consensus 39 ~~C~~~~C~~~f~~ 52 (151)
..| ..|+..|..
T Consensus 71 ~~C--~~Cg~~~~~ 82 (113)
T PRK12380 71 AWC--WDCSQVVEI 82 (113)
T ss_pred EEc--ccCCCEEec
Confidence 555 556654443
No 259
>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=23.61 E-value=31 Score=27.30 Aligned_cols=9 Identities=33% Similarity=0.955 Sum_probs=5.1
Q ss_pred ceeCCcCCc
Q psy4404 96 PFKCTICSH 104 (151)
Q Consensus 96 ~~~C~~C~~ 104 (151)
|..|+.|+.
T Consensus 253 ~~~Cp~C~s 261 (505)
T TIGR00595 253 PKTCPQCGS 261 (505)
T ss_pred CCCCCCCCC
Confidence 455666654
No 260
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.57 E-value=36 Score=21.15 Aligned_cols=14 Identities=21% Similarity=0.515 Sum_probs=9.9
Q ss_pred eeeccccccccccC
Q psy4404 3 LVICQYCEVRLESN 16 (151)
Q Consensus 3 ~~~C~~C~~~f~~~ 16 (151)
.+.|..||..|...
T Consensus 71 ~~~C~~Cg~~~~~~ 84 (117)
T PRK00564 71 ELECKDCSHVFKPN 84 (117)
T ss_pred EEEhhhCCCccccC
Confidence 46788888776543
No 261
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=23.54 E-value=32 Score=17.07 Aligned_cols=8 Identities=25% Similarity=0.555 Sum_probs=4.3
Q ss_pred eeeccccc
Q psy4404 3 LVICQYCE 10 (151)
Q Consensus 3 ~~~C~~C~ 10 (151)
+..||.||
T Consensus 2 ~~~Cp~Cg 9 (47)
T PF14690_consen 2 PPRCPHCG 9 (47)
T ss_pred CccCCCcC
Confidence 34556665
No 262
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=23.50 E-value=36 Score=20.20 Aligned_cols=14 Identities=14% Similarity=0.401 Sum_probs=9.2
Q ss_pred cceeeccCCCCcccCC
Q psy4404 37 FKYVCLYQKCSYHTGN 52 (151)
Q Consensus 37 ~~~~C~~~~C~~~f~~ 52 (151)
-.+.| ..|++.|.-
T Consensus 53 GIW~C--~~C~~~~AG 66 (90)
T PTZ00255 53 GIWRC--KGCKKTVAG 66 (90)
T ss_pred EEEEc--CCCCCEEeC
Confidence 45777 777776544
No 263
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.39 E-value=40 Score=22.69 Aligned_cols=34 Identities=26% Similarity=0.585 Sum_probs=19.4
Q ss_pred CCcceeeccCCCCcccCCchHHHHHHHhhcCCCceeCcccccccC
Q psy4404 35 VSFKYVCLYQKCSYHTGNSDHMRRHIRRHTGEKAFHCPHCEYRCS 79 (151)
Q Consensus 35 ~~~~~~C~~~~C~~~f~~~~~l~~h~~~h~~~~~~~C~~C~~~~~ 79 (151)
...-|.| +.|...++.-.++..- |.||.||....
T Consensus 110 ~~~~y~C--~~~~~r~sfdeA~~~~---------F~Cp~Cg~~L~ 143 (176)
T COG1675 110 ENNYYVC--PNCHVKYSFDEAMELG---------FTCPKCGEDLE 143 (176)
T ss_pred cCCceeC--CCCCCcccHHHHHHhC---------CCCCCCCchhh
Confidence 3445777 6666666555443322 66777776543
No 264
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=23.36 E-value=40 Score=24.61 Aligned_cols=9 Identities=33% Similarity=0.678 Sum_probs=5.1
Q ss_pred ecccccccc
Q psy4404 5 ICQYCEVRL 13 (151)
Q Consensus 5 ~C~~C~~~f 13 (151)
+|+.|+...
T Consensus 28 ~c~~c~~~~ 36 (285)
T TIGR00515 28 KCPKCGQVL 36 (285)
T ss_pred ECCCCcchh
Confidence 456665554
No 265
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=23.31 E-value=40 Score=19.02 Aligned_cols=23 Identities=22% Similarity=0.361 Sum_probs=14.8
Q ss_pred CceeeccccccccccCchHHHHH
Q psy4404 1 MILVICQYCEVRLESNSKELLEH 23 (151)
Q Consensus 1 ~~~~~C~~C~~~f~~~~~~l~~H 23 (151)
+.|..|..||+...+.-..+..-
T Consensus 2 iiPVRCFTCGkvig~~we~y~~~ 24 (71)
T PLN00032 2 IIPVRCFTCGKVIGNKWDTYLDL 24 (71)
T ss_pred CCceeecCCCCCcHHHHHHHHHH
Confidence 35777888888877665333333
No 266
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=23.19 E-value=29 Score=20.56 Aligned_cols=9 Identities=22% Similarity=0.781 Sum_probs=5.5
Q ss_pred CCCCcccCC
Q psy4404 44 QKCSYHTGN 52 (151)
Q Consensus 44 ~~C~~~f~~ 52 (151)
..||..|.+
T Consensus 62 kkCGfef~~ 70 (97)
T COG3357 62 KKCGFEFRD 70 (97)
T ss_pred cccCccccc
Confidence 566666655
No 267
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=22.90 E-value=49 Score=20.51 Aligned_cols=13 Identities=23% Similarity=0.463 Sum_probs=7.8
Q ss_pred eeecccccccccc
Q psy4404 3 LVICQYCEVRLES 15 (151)
Q Consensus 3 ~~~C~~C~~~f~~ 15 (151)
..+||.|++..+.
T Consensus 69 ~V~CP~C~K~TKm 81 (114)
T PF11023_consen 69 QVECPNCGKQTKM 81 (114)
T ss_pred eeECCCCCChHhh
Confidence 4567777666543
No 268
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=22.75 E-value=14 Score=18.26 Aligned_cols=17 Identities=41% Similarity=0.722 Sum_probs=6.4
Q ss_pred ccccccccccCchHHHHH
Q psy4404 6 CQYCEVRLESNSKELLEH 23 (151)
Q Consensus 6 C~~C~~~f~~~~~~l~~H 23 (151)
|+.||+.|.... .+..|
T Consensus 1 C~~C~~~~~~~~-~~~v~ 17 (47)
T PF01844_consen 1 CQYCGKPGSDNE-SLHVH 17 (47)
T ss_dssp -TTT--B--GG--GEEEE
T ss_pred CCCCCCcCccCc-ceEeE
Confidence 667777776654 44444
No 269
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=22.69 E-value=39 Score=20.06 Aligned_cols=13 Identities=23% Similarity=0.649 Sum_probs=8.0
Q ss_pred ceeeccCCCCcccCC
Q psy4404 38 KYVCLYQKCSYHTGN 52 (151)
Q Consensus 38 ~~~C~~~~C~~~f~~ 52 (151)
.+.| ..|++.|.-
T Consensus 54 IW~C--~~C~~~~AG 66 (90)
T PRK03976 54 IWEC--RKCGAKFAG 66 (90)
T ss_pred EEEc--CCCCCEEeC
Confidence 4667 667766543
No 270
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=22.41 E-value=82 Score=21.32 Aligned_cols=55 Identities=20% Similarity=0.413 Sum_probs=24.1
Q ss_pred ceeeccc----cccccccCchHHHHHHhhcCCCCCCCCCcceeecc--CCCCcccCCchHHHHHHHhhcCC
Q psy4404 2 ILVICQY----CEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLY--QKCSYHTGNSDHMRRHIRRHTGE 66 (151)
Q Consensus 2 ~~~~C~~----C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~--~~C~~~f~~~~~l~~h~~~h~~~ 66 (151)
..|+|+. |...|.. .....|.+.| .-.|+.||. ..|+..-.. ..|..|....+..
T Consensus 13 ~~~pC~~~~~GC~~~~~~--~~~~~HE~~C-------~~~p~~CP~~~~~C~~~G~~-~~l~~Hl~~~H~~ 73 (198)
T PF03145_consen 13 IKFPCKNAKYGCTETFPY--SEKREHEEEC-------PFRPCSCPFPGSGCDWQGSY-KELLDHLRDKHSW 73 (198)
T ss_dssp --EE-CCGGGT---EE-G--GGHHHHHHT--------TTSEEE-SSSSTT---EEEC-CCHHHHHHHHTTT
T ss_pred ceecCCCCCCCCcccccc--cChhhHhccC-------CCcCCcCCCCCCCccccCCH-HHHHHHHHHHCCC
Confidence 3466776 7777654 2566673221 224677765 557665543 4577776655544
No 271
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=22.11 E-value=36 Score=15.59 Aligned_cols=10 Identities=30% Similarity=0.657 Sum_probs=6.3
Q ss_pred eecccccccc
Q psy4404 4 VICQYCEVRL 13 (151)
Q Consensus 4 ~~C~~C~~~f 13 (151)
|.|..|++.+
T Consensus 28 f~C~~C~~~L 37 (39)
T smart00132 28 FKCSKCGKPL 37 (39)
T ss_pred CCCcccCCcC
Confidence 5566666655
No 272
>COG4896 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.90 E-value=52 Score=17.96 Aligned_cols=11 Identities=27% Similarity=0.875 Sum_probs=5.5
Q ss_pred cceeeccCCCCcc
Q psy4404 37 FKYVCLYQKCSYH 49 (151)
Q Consensus 37 ~~~~C~~~~C~~~ 49 (151)
..|.| ++|.-.
T Consensus 30 rtymC--~eC~~R 40 (68)
T COG4896 30 RTYMC--PECEHR 40 (68)
T ss_pred eeEec--hhhHhh
Confidence 34556 555433
No 273
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=21.77 E-value=79 Score=16.47 Aligned_cols=8 Identities=50% Similarity=1.564 Sum_probs=4.3
Q ss_pred eeeccCCCCc
Q psy4404 39 YVCLYQKCSY 48 (151)
Q Consensus 39 ~~C~~~~C~~ 48 (151)
+.| ..||.
T Consensus 38 ~~C--GkCgy 45 (51)
T COG1998 38 WAC--GKCGY 45 (51)
T ss_pred eEe--ccccc
Confidence 555 55554
No 274
>COG2879 Uncharacterized small protein [Function unknown]
Probab=21.65 E-value=1.1e+02 Score=16.87 Aligned_cols=19 Identities=21% Similarity=0.302 Sum_probs=14.2
Q ss_pred cCHHHHHHHHhhhcCCccc
Q psy4404 107 ARKDHMKRHLQLKHNADLS 125 (151)
Q Consensus 107 ~~~~~l~~H~~~~~~~~~~ 125 (151)
...+....||+.+++++|.
T Consensus 23 pdYdnYVehmr~~hPd~p~ 41 (65)
T COG2879 23 PDYDNYVEHMRKKHPDKPP 41 (65)
T ss_pred CcHHHHHHHHHHhCcCCCc
Confidence 3566778888888877765
No 275
>PTZ00448 hypothetical protein; Provisional
Probab=21.06 E-value=77 Score=24.07 Aligned_cols=23 Identities=17% Similarity=0.434 Sum_probs=20.7
Q ss_pred ceeCCcCCccccCHHHHHHHHhh
Q psy4404 96 PFKCTICSHKAARKDHMKRHLQL 118 (151)
Q Consensus 96 ~~~C~~C~~~f~~~~~l~~H~~~ 118 (151)
.|.|..|+-.|......+.|.++
T Consensus 314 ~~tC~~C~v~F~~~~~qR~H~KS 336 (373)
T PTZ00448 314 MLLCRKCNIQLMDHNAFKQHYRS 336 (373)
T ss_pred CccccccccccCCHHHHHHHhhh
Confidence 58899999999988999999886
No 276
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=20.97 E-value=49 Score=19.37 Aligned_cols=10 Identities=40% Similarity=0.906 Sum_probs=7.3
Q ss_pred eeeccccccc
Q psy4404 3 LVICQYCEVR 12 (151)
Q Consensus 3 ~~~C~~C~~~ 12 (151)
++.||.||..
T Consensus 1 lI~CP~CG~R 10 (84)
T PF04267_consen 1 LIPCPHCGPR 10 (84)
T ss_dssp EEEETTTEEE
T ss_pred CccCCCCCcc
Confidence 3678888884
No 277
>KOG2703|consensus
Probab=20.83 E-value=48 Score=25.46 Aligned_cols=11 Identities=18% Similarity=0.555 Sum_probs=8.6
Q ss_pred ceeeccccccc
Q psy4404 2 ILVICQYCEVR 12 (151)
Q Consensus 2 ~~~~C~~C~~~ 12 (151)
|.|.|++||-.
T Consensus 67 mSF~CpHCG~k 77 (460)
T KOG2703|consen 67 MSFECPHCGHK 77 (460)
T ss_pred EEeecCccCCc
Confidence 57888888865
No 278
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=20.35 E-value=89 Score=16.63 Aligned_cols=32 Identities=19% Similarity=0.469 Sum_probs=17.5
Q ss_pred eeccccccccccCchHHHHHHhhcCCCCCCCCCcceeeccCCCCc
Q psy4404 4 VICQYCEVRLESNSKELLEHCKTCKNLSRPDVSFKYVCLYQKCSY 48 (151)
Q Consensus 4 ~~C~~C~~~f~~~~~~l~~H~~~~~~~~~~~~~~~~~C~~~~C~~ 48 (151)
+.||.||..-+.+- - ..+--...|+.| +.|.+
T Consensus 5 i~CP~CgnKTR~ki-----r------~DT~LkNfPlyC--pKCK~ 36 (55)
T PF14205_consen 5 ILCPICGNKTRLKI-----R------EDTVLKNFPLYC--PKCKQ 36 (55)
T ss_pred EECCCCCCccceee-----e------cCceeccccccC--CCCCc
Confidence 45888886543332 1 223334556777 77754
No 279
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=20.21 E-value=1.4e+02 Score=15.77 Aligned_cols=8 Identities=38% Similarity=1.377 Sum_probs=4.0
Q ss_pred ceeCcccc
Q psy4404 68 AFHCPHCE 75 (151)
Q Consensus 68 ~~~C~~C~ 75 (151)
.|.|+.|+
T Consensus 44 ~y~C~~Cg 51 (54)
T PF10058_consen 44 QYRCPYCG 51 (54)
T ss_pred EEEcCCCC
Confidence 35555554
No 280
>PRK05978 hypothetical protein; Provisional
Probab=20.01 E-value=45 Score=21.80 Aligned_cols=7 Identities=29% Similarity=0.805 Sum_probs=3.2
Q ss_pred ccccccc
Q psy4404 6 CQYCEVR 12 (151)
Q Consensus 6 C~~C~~~ 12 (151)
||.||+.
T Consensus 36 CP~CG~G 42 (148)
T PRK05978 36 CPACGEG 42 (148)
T ss_pred CCCCCCC
Confidence 4444443
Done!