Query 043865
Match_columns 203
No_of_seqs 143 out of 1160
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 09:01:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043865.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043865hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1812 Predicted E3 ubiquitin 100.0 4.4E-32 9.5E-37 234.2 8.1 154 2-156 191-346 (384)
2 KOG1814 Predicted E3 ubiquitin 100.0 1.4E-31 3E-36 225.2 6.5 167 1-173 229-426 (445)
3 KOG0006 E3 ubiquitin-protein l 99.9 2E-24 4.3E-29 176.9 6.8 144 2-153 273-437 (446)
4 KOG1815 Predicted E3 ubiquitin 99.9 6E-24 1.3E-28 187.6 7.0 158 2-165 114-283 (444)
5 smart00647 IBR In Between Ring 99.5 6.4E-14 1.4E-18 91.3 5.4 63 28-93 1-64 (64)
6 PF01485 IBR: IBR domain; Int 99.5 1.3E-14 2.8E-19 94.6 0.9 63 28-93 1-64 (64)
7 smart00647 IBR In Between Ring 98.7 3.7E-08 8E-13 63.8 5.1 50 105-154 6-61 (64)
8 PF01485 IBR: IBR domain; Int 98.5 4.2E-08 9.1E-13 63.5 0.9 41 114-154 16-61 (64)
9 KOG1814 Predicted E3 ubiquitin 95.8 0.0023 4.9E-08 55.4 -0.3 46 115-160 272-320 (445)
10 PF10571 UPF0547: Uncharacteri 95.2 0.0087 1.9E-07 31.6 0.8 23 117-143 1-24 (26)
11 KOG1812 Predicted E3 ubiquitin 94.2 0.031 6.8E-07 48.9 2.5 43 42-92 304-346 (384)
12 PF13719 zinc_ribbon_5: zinc-r 93.3 0.087 1.9E-06 30.2 2.4 33 44-79 2-35 (37)
13 PF13717 zinc_ribbon_4: zinc-r 92.8 0.12 2.6E-06 29.4 2.5 33 44-79 2-35 (36)
14 KOG1815 Predicted E3 ubiquitin 92.5 0.097 2.1E-06 46.7 2.7 45 116-160 158-205 (444)
15 smart00661 RPOL9 RNA polymeras 92.2 0.11 2.3E-06 31.8 1.9 27 117-143 1-30 (52)
16 PF13248 zf-ribbon_3: zinc-rib 92.0 0.075 1.6E-06 27.9 0.9 23 117-150 3-25 (26)
17 PF09889 DUF2116: Uncharacteri 91.8 0.21 4.6E-06 31.8 2.9 26 117-153 4-30 (59)
18 PF13240 zinc_ribbon_2: zinc-r 91.5 0.084 1.8E-06 27.0 0.7 11 118-128 1-11 (23)
19 PRK00432 30S ribosomal protein 91.2 0.14 3E-06 31.5 1.6 27 115-143 19-47 (50)
20 PHA00626 hypothetical protein 90.8 0.19 4.1E-06 31.4 1.9 26 118-143 2-33 (59)
21 TIGR02098 MJ0042_CXXC MJ0042 f 90.7 0.29 6.3E-06 27.9 2.5 32 45-79 3-35 (38)
22 PRK00398 rpoP DNA-directed RNA 90.4 0.24 5.2E-06 29.6 2.1 29 117-145 4-33 (46)
23 PLN03086 PRLI-interacting fact 89.7 0.65 1.4E-05 42.6 5.2 56 2-79 408-463 (567)
24 COG1998 RPS31 Ribosomal protei 88.7 0.28 6E-06 29.9 1.4 27 115-141 18-45 (51)
25 PF09297 zf-NADH-PPase: NADH p 88.4 0.57 1.2E-05 25.7 2.5 27 116-142 3-30 (32)
26 PF07975 C1_4: TFIIH C1-like d 86.4 0.27 5.9E-06 30.3 0.4 25 67-91 19-43 (51)
27 KOG2906 RNA polymerase III sub 85.2 0.71 1.5E-05 32.3 2.1 29 118-146 3-34 (105)
28 PF02150 RNA_POL_M_15KD: RNA p 84.8 0.66 1.4E-05 26.2 1.5 28 45-78 2-29 (35)
29 smart00661 RPOL9 RNA polymeras 84.5 0.84 1.8E-05 27.7 2.1 28 46-78 2-29 (52)
30 PHA03049 IMV membrane protein; 83.8 1.6 3.5E-05 28.2 3.1 22 175-196 3-24 (68)
31 PRK00398 rpoP DNA-directed RNA 82.8 1.9 4.2E-05 25.6 3.1 29 45-80 4-32 (46)
32 PF01599 Ribosomal_S27: Riboso 82.2 1.1 2.5E-05 27.0 1.9 30 43-77 17-46 (47)
33 COG2888 Predicted Zn-ribbon RN 81.8 1.1 2.3E-05 28.5 1.7 33 45-84 10-42 (61)
34 KOG0006 E3 ubiquitin-protein l 81.8 1.3 2.8E-05 37.6 2.7 40 43-89 396-437 (446)
35 PF05961 Chordopox_A13L: Chord 81.6 2.2 4.8E-05 27.7 3.1 24 175-198 3-26 (68)
36 PF09788 Tmemb_55A: Transmembr 80.8 11 0.00023 31.1 7.6 45 117-162 124-185 (256)
37 PF03119 DNA_ligase_ZBD: NAD-d 80.2 1.9 4.1E-05 23.0 2.1 20 118-137 1-20 (28)
38 PF14569 zf-UDP: Zinc-binding 79.9 0.73 1.6E-05 30.8 0.5 46 65-134 24-69 (80)
39 PF14353 CpXC: CpXC protein 79.5 1.5 3.3E-05 32.1 2.2 27 103-129 23-51 (128)
40 PF14803 Nudix_N_2: Nudix N-te 78.7 1.9 4.1E-05 24.2 1.9 25 117-141 1-30 (34)
41 PF08274 PhnA_Zn_Ribbon: PhnA 78.6 1.6 3.5E-05 23.8 1.5 25 118-143 4-29 (30)
42 PF09680 Tiny_TM_bacill: Prote 77.8 2.3 4.9E-05 21.8 1.8 16 174-189 6-21 (24)
43 PF07282 OrfB_Zn_ribbon: Putat 77.8 1.7 3.7E-05 28.1 1.8 28 115-142 27-55 (69)
44 smart00531 TFIIE Transcription 77.6 3.7 8E-05 30.9 3.9 36 41-78 96-132 (147)
45 PRK08665 ribonucleotide-diphos 77.3 1.4 3E-05 42.1 1.8 26 117-144 725-751 (752)
46 MTH00261 ATP8 ATP synthase F0 76.9 4 8.6E-05 25.5 3.1 25 174-198 14-38 (68)
47 KOG0317 Predicted E3 ubiquitin 76.6 0.44 9.5E-06 39.8 -1.5 33 116-154 239-272 (293)
48 PF09538 FYDLN_acid: Protein o 76.5 1.4 3E-05 31.6 1.2 26 117-143 10-36 (108)
49 PF07191 zinc-ribbons_6: zinc- 76.1 2.3 4.9E-05 28.0 2.0 34 118-153 3-42 (70)
50 PRK14559 putative protein seri 75.7 1.3 2.8E-05 41.5 1.1 32 116-153 15-53 (645)
51 PF14952 zf-tcix: Putative tre 75.3 1.6 3.4E-05 25.9 1.0 27 113-143 8-37 (44)
52 TIGR02972 TMAO_torE trimethyla 75.2 11 0.00023 22.8 4.6 30 168-197 8-37 (47)
53 TIGR00622 ssl1 transcription f 75.2 2.2 4.8E-05 30.7 1.9 45 45-91 56-103 (112)
54 PLN03208 E3 ubiquitin-protein 75.1 0.6 1.3E-05 36.9 -1.1 35 113-152 15-49 (193)
55 PRK05654 acetyl-CoA carboxylas 75.1 0.56 1.2E-05 39.6 -1.3 30 114-143 25-56 (292)
56 COG1198 PriA Primosomal protei 74.9 2.6 5.6E-05 40.1 2.8 34 117-150 445-484 (730)
57 TIGR01384 TFS_arch transcripti 74.9 1.9 4.2E-05 30.3 1.6 24 118-143 2-26 (104)
58 TIGR01732 tiny_TM_bacill conse 74.5 3.8 8.2E-05 21.4 2.2 15 175-189 9-23 (26)
59 COG4640 Predicted membrane pro 73.9 4.2 9.1E-05 35.6 3.6 23 172-194 51-73 (465)
60 PF06677 Auto_anti-p27: Sjogre 73.3 3.4 7.4E-05 24.2 2.1 23 116-140 17-41 (41)
61 PRK06266 transcription initiat 72.8 4.4 9.6E-05 31.6 3.3 60 13-78 85-145 (178)
62 KOG0823 Predicted E3 ubiquitin 72.6 0.94 2E-05 36.6 -0.5 16 138-153 64-79 (230)
63 TIGR00373 conserved hypothetic 72.5 4.2 9.1E-05 31.1 3.1 60 13-78 77-137 (158)
64 PF13923 zf-C3HC4_2: Zinc fing 72.4 0.82 1.8E-05 26.1 -0.7 20 134-153 11-31 (39)
65 PF15227 zf-C3HC4_4: zinc fing 72.0 1 2.3E-05 26.4 -0.3 20 134-153 11-30 (42)
66 PF06827 zf-FPG_IleRS: Zinc fi 71.8 3.5 7.5E-05 22.1 1.8 24 117-140 2-28 (30)
67 PHA02926 zinc finger-like prot 71.3 1 2.2E-05 36.4 -0.6 37 73-128 195-231 (242)
68 CHL00174 accD acetyl-CoA carbo 71.3 0.76 1.6E-05 38.8 -1.4 30 115-144 37-68 (296)
69 PF14149 YhfH: YhfH-like prote 71.3 0.34 7.3E-06 27.7 -2.4 31 109-139 6-37 (37)
70 PF06796 NapE: Periplasmic nit 70.9 17 0.00036 22.8 4.9 31 167-197 15-45 (56)
71 PF02748 PyrI_C: Aspartate car 70.9 3.9 8.5E-05 25.2 2.1 35 43-78 5-44 (52)
72 TIGR00515 accD acetyl-CoA carb 70.6 0.84 1.8E-05 38.4 -1.3 30 114-143 24-55 (285)
73 COG1594 RPB9 DNA-directed RNA 70.2 4.4 9.6E-05 29.2 2.6 30 44-78 2-31 (113)
74 PF13639 zf-RING_2: Ring finge 68.5 0.98 2.1E-05 26.4 -1.0 33 119-153 3-35 (44)
75 PF10661 EssA: WXG100 protein 68.4 7.2 0.00016 29.5 3.5 19 184-202 126-144 (145)
76 PF12773 DZR: Double zinc ribb 68.3 2.4 5.1E-05 25.5 0.7 12 116-127 29-40 (50)
77 COG3763 Uncharacterized protei 68.2 9.5 0.0002 25.0 3.5 23 178-200 6-28 (71)
78 PLN02638 cellulose synthase A 66.9 3.4 7.4E-05 40.7 1.8 20 65-84 32-51 (1079)
79 PF00097 zf-C3HC4: Zinc finger 66.4 0.93 2E-05 26.0 -1.4 16 138-153 16-31 (41)
80 KOG0823 Predicted E3 ubiquitin 65.3 2.4 5.2E-05 34.4 0.4 21 65-87 57-77 (230)
81 PF12760 Zn_Tnp_IS1595: Transp 65.0 17 0.00038 21.4 4.1 26 117-142 19-46 (46)
82 KOG2041 WD40 repeat protein [G 65.0 7.3 0.00016 37.0 3.4 50 19-79 1086-1141(1189)
83 PRK14714 DNA polymerase II lar 64.8 6.3 0.00014 39.5 3.2 18 69-86 667-688 (1337)
84 PRK09710 lar restriction allev 64.8 7.1 0.00015 25.2 2.4 28 115-142 5-36 (64)
85 PLN02189 cellulose synthase 64.6 4.6 0.0001 39.6 2.2 20 65-84 49-68 (1040)
86 PLN03086 PRLI-interacting fact 64.2 4.1 9E-05 37.5 1.7 29 115-143 432-463 (567)
87 PRK14892 putative transcriptio 64.0 6.1 0.00013 27.9 2.2 29 115-143 20-52 (99)
88 TIGR02443 conserved hypothetic 64.0 8.1 0.00018 24.5 2.5 25 118-142 11-40 (59)
89 cd00162 RING RING-finger (Real 63.7 2.3 4.9E-05 24.0 -0.0 30 119-153 2-32 (45)
90 PF10122 Mu-like_Com: Mu-like 63.5 2.6 5.6E-05 25.9 0.2 24 118-141 6-32 (51)
91 PF09526 DUF2387: Probable met 63.3 7.7 0.00017 25.6 2.4 25 118-142 10-39 (71)
92 PF01363 FYVE: FYVE zinc finge 62.7 4.3 9.3E-05 26.1 1.2 38 113-152 6-44 (69)
93 COG3630 OadG Na+-transporting 62.7 17 0.00038 24.7 4.1 27 174-200 15-41 (84)
94 PRK00420 hypothetical protein; 62.6 5.7 0.00012 28.7 1.9 30 115-153 22-52 (112)
95 COG0777 AccD Acetyl-CoA carbox 62.5 2.7 5.8E-05 35.1 0.2 33 113-145 25-59 (294)
96 TIGR02973 nitrate_rd_NapE peri 62.3 28 0.00061 20.5 4.4 28 169-196 4-31 (42)
97 PF06024 DUF912: Nucleopolyhed 61.9 4.6 0.0001 28.5 1.3 18 178-198 68-85 (101)
98 PRK14559 putative protein seri 61.4 6.7 0.00015 36.9 2.6 14 114-127 39-52 (645)
99 PLN02400 cellulose synthase 61.0 6.5 0.00014 38.8 2.5 20 65-84 51-70 (1085)
100 KOG4684 Uncharacterized conser 60.7 9.3 0.0002 30.7 2.9 21 41-61 135-155 (275)
101 PRK02935 hypothetical protein; 60.6 6.4 0.00014 28.0 1.8 24 65-88 66-97 (110)
102 PF11023 DUF2614: Protein of u 60.5 6 0.00013 28.5 1.6 25 65-89 65-97 (114)
103 PRK14750 kdpF potassium-transp 60.5 23 0.0005 18.9 3.4 10 185-194 14-23 (29)
104 TIGR03655 anti_R_Lar restricti 60.1 7.8 0.00017 23.8 2.0 11 117-127 2-12 (53)
105 PF08746 zf-RING-like: RING-li 59.8 9.4 0.0002 22.4 2.2 14 109-122 30-43 (43)
106 PRK14890 putative Zn-ribbon RN 59.6 6.6 0.00014 24.9 1.5 27 46-79 9-35 (59)
107 PF08271 TF_Zn_Ribbon: TFIIB z 59.5 11 0.00023 22.0 2.4 8 118-125 2-9 (43)
108 COG1997 RPL43A Ribosomal prote 59.2 7.8 0.00017 26.6 1.9 28 116-143 35-63 (89)
109 PF12911 OppC_N: N-terminal TM 59.0 11 0.00023 23.1 2.5 22 167-188 13-34 (56)
110 PLN02436 cellulose synthase A 58.7 6.9 0.00015 38.6 2.2 47 65-135 51-97 (1094)
111 COG1594 RPB9 DNA-directed RNA 58.4 9.4 0.0002 27.5 2.4 27 117-143 3-32 (113)
112 PHA02929 N1R/p28-like protein; 58.1 3.4 7.4E-05 33.8 0.1 16 73-88 198-213 (238)
113 PF01428 zf-AN1: AN1-like Zinc 57.5 6.2 0.00013 23.1 1.1 28 68-97 12-39 (43)
114 COG1645 Uncharacterized Zn-fin 57.4 9.5 0.00021 28.3 2.3 25 115-148 27-51 (131)
115 PF14835 zf-RING_6: zf-RING of 57.3 6.7 0.00014 25.4 1.3 22 116-137 7-31 (65)
116 PF09788 Tmemb_55A: Transmembr 57.0 13 0.00029 30.6 3.3 39 41-79 120-167 (256)
117 smart00659 RPOLCX RNA polymera 56.0 11 0.00024 22.3 2.0 11 117-127 20-30 (44)
118 PF05129 Elf1: Transcription e 55.9 8.3 0.00018 26.1 1.7 29 115-143 21-56 (81)
119 KOG2906 RNA polymerase III sub 55.6 11 0.00024 26.5 2.2 29 45-78 2-30 (105)
120 KOG0317 Predicted E3 ubiquitin 55.4 2.4 5.3E-05 35.4 -1.2 20 70-89 252-271 (293)
121 TIGR00686 phnA alkylphosphonat 55.2 9.2 0.0002 27.3 1.8 26 117-143 3-29 (109)
122 PF13453 zf-TFIIB: Transcripti 55.0 8.5 0.00018 22.2 1.4 13 118-130 1-13 (41)
123 PF07754 DUF1610: Domain of un 54.6 10 0.00022 19.5 1.5 11 67-77 14-24 (24)
124 PF11395 DUF2873: Protein of u 54.3 28 0.0006 19.9 3.3 17 176-192 14-30 (43)
125 KOG2927 Membrane component of 53.9 8.9 0.00019 33.1 1.9 19 177-195 192-210 (372)
126 PLN00209 ribosomal protein S27 53.8 20 0.00044 24.5 3.3 31 45-81 37-67 (86)
127 PF12606 RELT: Tumour necrosis 53.8 9.6 0.00021 23.4 1.5 15 177-191 6-20 (50)
128 COG2051 RPS27A Ribosomal prote 53.5 16 0.00034 23.7 2.6 32 44-81 19-50 (67)
129 TIGR02300 FYDLN_acid conserved 52.8 8 0.00017 28.5 1.3 26 117-143 10-36 (129)
130 PTZ00083 40S ribosomal protein 52.5 21 0.00047 24.3 3.2 31 45-81 36-66 (85)
131 PF08792 A2L_zn_ribbon: A2L zi 52.5 14 0.0003 20.5 1.9 25 117-141 4-29 (33)
132 TIGR00595 priA primosomal prot 52.2 12 0.00027 34.0 2.6 33 118-150 224-262 (505)
133 PLN02915 cellulose synthase A 51.6 10 0.00022 37.5 2.0 20 65-84 30-49 (1044)
134 KOG4367 Predicted Zn-finger pr 51.5 3.6 7.8E-05 36.5 -0.8 80 67-153 174-255 (699)
135 PF10083 DUF2321: Uncharacteri 50.6 4 8.7E-05 31.1 -0.6 39 114-152 37-79 (158)
136 smart00184 RING Ring finger. E 50.3 5.5 0.00012 21.4 0.1 16 138-153 15-30 (39)
137 PF02468 PsbN: Photosystem II 49.0 19 0.00042 21.3 2.2 19 180-198 9-27 (43)
138 PF07243 Phlebovirus_G1: Phleb 48.7 32 0.00068 31.5 4.6 56 139-201 399-454 (526)
139 PRK10220 hypothetical protein; 48.2 15 0.00032 26.3 2.0 26 117-143 4-30 (111)
140 PHA02929 N1R/p28-like protein; 48.1 8.5 0.00018 31.6 0.9 39 115-153 173-214 (238)
141 PF01405 PsbT: Photosystem II 47.8 42 0.00091 18.0 3.2 17 179-195 6-22 (29)
142 PRK03681 hypA hydrogenase nick 47.8 37 0.00079 24.4 4.1 48 23-78 40-96 (114)
143 PF14354 Lar_restr_allev: Rest 47.4 17 0.00036 22.6 2.0 27 115-141 2-37 (61)
144 COG2816 NPY1 NTP pyrophosphohy 47.2 30 0.00065 29.0 4.0 56 15-79 83-139 (279)
145 PHA02926 zinc finger-like prot 47.2 9.3 0.0002 31.0 0.9 46 109-154 163-212 (242)
146 PRK11875 psbT photosystem II r 46.9 37 0.00081 18.5 2.9 17 179-195 6-22 (31)
147 TIGR00100 hypA hydrogenase nic 46.9 38 0.00082 24.3 4.0 27 42-77 68-94 (115)
148 PF09451 ATG27: Autophagy-rela 46.8 20 0.00042 29.8 2.9 24 176-199 204-227 (268)
149 TIGR01206 lysW lysine biosynth 46.3 26 0.00057 21.8 2.7 29 46-79 4-32 (54)
150 PF15061 DUF4538: Domain of un 46.3 23 0.0005 22.3 2.4 17 180-196 11-27 (58)
151 COG4897 CsbA Uncharacterized p 46.0 47 0.001 21.9 3.9 26 173-198 4-29 (78)
152 PF13908 Shisa: Wnt and FGF in 45.8 20 0.00044 27.7 2.6 15 133-147 25-41 (179)
153 PF10426 zf-RAG1: Recombinatio 45.6 3.3 7.1E-05 22.5 -1.3 20 2-21 3-22 (30)
154 PF01788 PsbJ: PsbJ; InterPro 45.3 25 0.00054 20.4 2.2 16 181-196 19-34 (40)
155 PRK03824 hypA hydrogenase nick 44.7 43 0.00093 24.8 4.2 35 23-59 40-83 (135)
156 PF14570 zf-RING_4: RING/Ubox 44.7 5.4 0.00012 24.2 -0.6 34 119-153 1-34 (48)
157 PRK00893 aspartate carbamoyltr 44.6 25 0.00054 26.8 2.9 38 42-79 103-144 (152)
158 PRK12380 hydrogenase nickel in 44.4 43 0.00093 24.0 4.0 47 22-77 39-94 (113)
159 CHL00031 psbT photosystem II p 43.4 34 0.00075 18.9 2.5 17 179-195 6-22 (33)
160 COG1781 PyrI Aspartate carbamo 43.3 23 0.0005 26.9 2.5 38 41-78 103-144 (153)
161 PF14446 Prok-RING_1: Prokaryo 43.2 15 0.00032 22.9 1.2 10 69-78 21-30 (54)
162 PF01214 CK_II_beta: Casein ki 42.9 49 0.0011 26.0 4.4 38 41-78 96-136 (184)
163 KOG1726 HVA22/DP1 gene product 42.8 39 0.00084 27.5 3.9 33 170-202 37-69 (225)
164 COG0266 Nei Formamidopyrimidin 42.8 20 0.00043 30.0 2.3 24 117-140 246-272 (273)
165 PRK14748 kdpF potassium-transp 42.4 55 0.0012 17.5 3.5 19 173-194 5-23 (29)
166 PF03604 DNA_RNApol_7kD: DNA d 42.4 9.3 0.0002 21.1 0.2 11 116-126 17-27 (32)
167 PRK14873 primosome assembly pr 42.2 20 0.00043 34.0 2.4 34 117-150 393-431 (665)
168 PF02591 DUF164: Putative zinc 41.6 17 0.00037 22.4 1.3 21 105-125 35-55 (56)
169 KOG4007 Uncharacterized conser 41.2 8.9 0.00019 30.3 0.0 17 182-198 139-156 (229)
170 PRK14714 DNA polymerase II lar 41.1 16 0.00035 36.8 1.7 31 117-153 668-704 (1337)
171 COG1579 Zn-ribbon protein, pos 41.0 26 0.00057 28.7 2.7 61 16-78 166-230 (239)
172 PRK14811 formamidopyrimidine-D 40.8 23 0.00049 29.5 2.4 25 117-148 236-262 (269)
173 COG3677 Transposase and inacti 40.8 33 0.00071 25.3 3.0 39 41-81 27-65 (129)
174 PF00098 zf-CCHC: Zinc knuckle 40.5 26 0.00056 16.5 1.6 16 79-94 2-17 (18)
175 PF13913 zf-C2HC_2: zinc-finge 40.4 14 0.0003 19.0 0.7 11 69-79 2-12 (25)
176 PF01530 zf-C2HC: Zinc finger, 40.3 17 0.00036 20.0 1.0 12 1-12 1-12 (31)
177 PF10497 zf-4CXXC_R1: Zinc-fin 40.0 16 0.00035 25.9 1.2 17 107-124 53-69 (105)
178 PF12428 DUF3675: Protein of u 39.9 42 0.00092 24.4 3.4 14 188-201 104-117 (118)
179 PRK05580 primosome assembly pr 39.8 24 0.00052 33.4 2.6 33 118-150 392-430 (679)
180 PRK01103 formamidopyrimidine/5 39.8 25 0.00054 29.3 2.5 13 117-129 246-258 (274)
181 PF05767 Pox_A14: Poxvirus vir 39.5 91 0.002 21.6 4.7 23 173-195 46-68 (92)
182 TIGR00240 ATCase_reg aspartate 39.4 29 0.00063 26.4 2.5 38 42-79 101-142 (150)
183 PRK04023 DNA polymerase II lar 39.0 28 0.00062 34.4 2.9 33 115-153 625-663 (1121)
184 PRK00415 rps27e 30S ribosomal 38.8 41 0.00088 21.3 2.7 30 45-80 12-41 (59)
185 COG1096 Predicted RNA-binding 38.3 22 0.00047 28.0 1.7 23 117-141 150-173 (188)
186 KOG0978 E3 ubiquitin ligase in 38.3 6 0.00013 37.3 -1.5 13 114-126 676-688 (698)
187 COG1996 RPC10 DNA-directed RNA 38.2 18 0.0004 22.0 1.1 13 115-127 23-35 (49)
188 TIGR01053 LSD1 zinc finger dom 38.1 40 0.00086 18.4 2.3 24 118-141 3-27 (31)
189 PLN02195 cellulose synthase A 38.0 22 0.00047 35.0 2.0 21 65-85 21-41 (977)
190 PRK11827 hypothetical protein; 37.9 29 0.00062 22.1 1.9 27 116-142 8-35 (60)
191 smart00834 CxxC_CXXC_SSSS Puta 37.7 19 0.00041 20.3 1.1 14 116-129 26-39 (41)
192 PRK10445 endonuclease VIII; Pr 37.6 27 0.0006 28.9 2.4 21 117-137 236-258 (263)
193 PF09723 Zn-ribbon_8: Zinc rib 37.0 38 0.00083 19.6 2.3 28 46-77 7-34 (42)
194 PF15052 TMEM169: TMEM169 prot 37.0 44 0.00096 24.6 3.0 38 164-201 53-90 (133)
195 COG2816 NPY1 NTP pyrophosphohy 36.8 33 0.00071 28.8 2.7 30 114-143 109-139 (279)
196 PRK14810 formamidopyrimidine-D 36.8 28 0.00062 28.9 2.4 13 117-129 245-257 (272)
197 PRK00523 hypothetical protein; 36.7 67 0.0014 21.2 3.6 14 184-197 13-26 (72)
198 PF15616 TerY-C: TerY-C metal 36.4 21 0.00046 26.5 1.3 26 115-146 76-101 (131)
199 PRK00241 nudC NADH pyrophospha 36.3 66 0.0014 26.5 4.4 32 41-79 96-127 (256)
200 PF04277 OAD_gamma: Oxaloaceta 36.3 78 0.0017 20.7 4.1 21 174-194 9-29 (79)
201 COG4306 Uncharacterized protei 36.3 41 0.0009 24.8 2.8 50 23-79 23-78 (160)
202 COG3296 Uncharacterized protei 36.3 80 0.0017 23.4 4.3 16 185-200 108-123 (143)
203 TIGR03826 YvyF flagellar opero 36.1 16 0.00035 27.3 0.7 24 117-152 82-105 (137)
204 PRK04023 DNA polymerase II lar 36.0 34 0.00073 33.9 2.9 20 69-88 638-662 (1121)
205 PF01102 Glycophorin_A: Glycop 36.0 65 0.0014 23.6 3.8 20 178-197 69-88 (122)
206 PF05434 Tmemb_9: TMEM9; Inte 35.9 23 0.0005 26.8 1.5 16 183-198 61-77 (149)
207 KOG1039 Predicted E3 ubiquitin 35.9 14 0.0003 32.0 0.3 17 73-89 185-201 (344)
208 PF14634 zf-RING_5: zinc-RING 35.7 16 0.00034 21.3 0.5 33 118-152 1-33 (44)
209 TIGR01195 oadG_fam sodium pump 35.7 82 0.0018 21.2 4.1 20 175-194 13-32 (82)
210 PF13465 zf-H2C2_2: Zinc-finge 35.7 26 0.00056 17.9 1.3 13 67-79 12-24 (26)
211 PHA02692 hypothetical protein; 35.1 79 0.0017 20.7 3.7 19 177-195 48-66 (70)
212 TIGR00577 fpg formamidopyrimid 35.1 31 0.00067 28.7 2.3 13 117-129 246-258 (272)
213 PF14169 YdjO: Cold-inducible 34.9 32 0.0007 21.8 1.8 32 42-77 16-47 (59)
214 PF08882 Acetone_carb_G: Aceto 34.8 29 0.00063 24.9 1.8 20 133-153 23-42 (112)
215 PHA03099 epidermal growth fact 34.8 46 0.001 24.6 2.8 24 177-200 105-128 (139)
216 PF05715 zf-piccolo: Piccolo Z 34.7 19 0.00041 22.9 0.7 38 117-154 3-43 (61)
217 PF09527 ATPase_gene1: Putativ 34.4 55 0.0012 19.9 2.9 21 181-201 34-54 (55)
218 PF07010 Endomucin: Endomucin; 34.4 62 0.0013 26.4 3.8 28 173-200 189-216 (259)
219 PF06716 DUF1201: Protein of u 34.3 1.1E+02 0.0023 18.4 3.9 15 189-203 23-37 (54)
220 PF01155 HypA: Hydrogenase exp 34.2 35 0.00075 24.4 2.2 48 22-78 39-95 (113)
221 PRK13183 psbN photosystem II r 34.2 36 0.00077 20.4 1.8 19 180-198 12-30 (46)
222 PF14319 Zn_Tnp_IS91: Transpos 34.1 1.1E+02 0.0024 21.8 4.8 49 22-85 19-68 (111)
223 PRK13945 formamidopyrimidine-D 34.0 32 0.00068 28.8 2.2 21 117-137 255-277 (282)
224 PF14369 zf-RING_3: zinc-finge 34.0 62 0.0013 18.0 2.7 29 45-79 3-31 (35)
225 TIGR00595 priA primosomal prot 33.7 72 0.0016 29.1 4.6 62 20-86 181-262 (505)
226 smart00064 FYVE Protein presen 33.6 18 0.00039 23.0 0.6 37 115-153 9-46 (68)
227 PF04216 FdhE: Protein involve 33.5 25 0.00055 29.4 1.6 34 117-150 173-220 (290)
228 PF12459 DUF3687: D-Ala-teicho 33.0 1.1E+02 0.0023 18.0 3.8 23 171-193 7-29 (42)
229 PRK09521 exosome complex RNA-b 32.9 32 0.0007 26.9 2.0 24 118-142 151-175 (189)
230 PF01667 Ribosomal_S27e: Ribos 32.8 60 0.0013 20.3 2.8 32 44-81 7-38 (55)
231 PRK00241 nudC NADH pyrophospha 32.7 30 0.00066 28.5 1.9 28 115-142 98-126 (256)
232 PRK01844 hypothetical protein; 32.6 86 0.0019 20.7 3.6 15 184-198 12-26 (72)
233 PF09125 COX2-transmemb: Cytoc 32.4 1E+02 0.0022 17.5 3.8 21 169-189 13-33 (38)
234 PF13920 zf-C3HC4_3: Zinc fing 32.3 37 0.0008 20.1 1.8 14 115-128 36-49 (50)
235 PTZ00396 Casein kinase II subu 32.2 86 0.0019 26.0 4.4 37 41-77 117-156 (251)
236 COG1198 PriA Primosomal protei 32.1 1E+02 0.0022 29.6 5.4 60 22-86 405-484 (730)
237 PLN00063 photosystem II core c 31.8 48 0.001 26.0 2.6 20 176-195 162-181 (194)
238 COG5574 PEX10 RING-finger-cont 31.8 10 0.00022 31.4 -1.0 30 118-153 217-248 (271)
239 PF06943 zf-LSD1: LSD1 zinc fi 31.5 57 0.0012 16.9 2.1 23 119-141 1-24 (25)
240 PF11781 RRN7: RNA polymerase 30.7 46 0.001 18.7 1.9 24 117-142 9-34 (36)
241 PF01927 Mut7-C: Mut7-C RNAse 30.6 90 0.002 23.3 4.0 53 25-79 69-134 (147)
242 PF12677 DUF3797: Domain of un 30.4 55 0.0012 19.9 2.2 27 116-142 13-47 (49)
243 KOG2164 Predicted E3 ubiquitin 30.4 21 0.00045 32.4 0.6 34 74-128 203-237 (513)
244 PRK00564 hypA hydrogenase nick 30.3 73 0.0016 22.9 3.3 48 22-77 39-96 (117)
245 COG3529 Predicted nucleic-acid 30.2 14 0.00031 23.5 -0.4 26 118-143 12-42 (66)
246 PF09604 Potass_KdpF: F subuni 30.2 71 0.0015 16.5 2.3 15 185-199 7-21 (25)
247 COG5232 SEC62 Preprotein trans 29.8 33 0.00072 27.6 1.5 13 182-194 158-170 (259)
248 TIGR03037 anthran_nbaC 3-hydro 29.6 27 0.00059 26.8 1.0 45 77-124 114-159 (159)
249 PF15361 RIC3: Resistance to i 29.3 40 0.00086 25.6 1.9 15 186-200 90-104 (152)
250 PF11789 zf-Nse: Zinc-finger o 29.2 29 0.00063 21.7 0.9 14 40-53 44-57 (57)
251 smart00734 ZnF_Rad18 Rad18-lik 29.1 29 0.00062 18.0 0.7 20 2-23 2-21 (26)
252 PF00643 zf-B_box: B-box zinc 29.1 19 0.0004 20.5 0.0 25 67-91 13-37 (42)
253 KOG3092 Casein kinase II, beta 28.9 84 0.0018 25.0 3.6 41 41-81 103-146 (216)
254 cd00021 BBOX B-Box-type zinc f 28.9 37 0.0008 18.6 1.3 25 67-91 10-34 (39)
255 TIGR02115 potass_kdpF K+-trans 28.7 74 0.0016 16.7 2.3 15 185-199 6-20 (26)
256 COG1675 TFA1 Transcription ini 28.7 42 0.0009 26.2 1.9 31 41-77 110-140 (176)
257 PF00096 zf-C2H2: Zinc finger, 28.5 28 0.0006 16.8 0.6 9 71-79 2-10 (23)
258 PF11346 DUF3149: Protein of u 28.4 1.3E+02 0.0028 17.6 3.6 26 176-201 12-37 (42)
259 PRK12286 rpmF 50S ribosomal pr 28.4 34 0.00074 21.4 1.2 23 114-141 25-48 (57)
260 CHL00020 psbN photosystem II p 28.3 38 0.00082 20.0 1.2 19 180-198 9-27 (43)
261 PF13153 DUF3985: Protein of u 28.3 1E+02 0.0022 17.8 2.9 11 171-181 4-14 (44)
262 PRK08332 ribonucleotide-diphos 28.2 37 0.00079 35.7 1.9 27 117-145 1705-1738(1740)
263 PRK08115 ribonucleotide-diphos 27.7 30 0.00064 33.7 1.1 24 117-142 828-853 (858)
264 PRK13264 3-hydroxyanthranilate 27.6 29 0.00064 27.1 0.9 51 76-129 119-170 (177)
265 PF01396 zf-C4_Topoisom: Topoi 27.2 43 0.00093 19.1 1.3 20 117-137 2-24 (39)
266 smart00154 ZnF_AN1 AN1-like Zi 27.2 42 0.00092 19.2 1.3 18 69-86 12-29 (39)
267 PF01529 zf-DHHC: DHHC palmito 27.1 2.1E+02 0.0045 21.4 5.6 39 113-162 45-84 (174)
268 PF06084 Cytomega_TRL10: Cytom 27.0 74 0.0016 23.0 2.8 12 130-141 15-26 (150)
269 PF01873 eIF-5_eIF-2B: Domain 26.9 1E+02 0.0022 22.5 3.6 29 114-142 91-123 (125)
270 PF06143 Baculo_11_kDa: Baculo 26.2 1.4E+02 0.003 20.4 3.8 18 181-198 43-60 (84)
271 PF02318 FYVE_2: FYVE-type zin 26.2 54 0.0012 23.5 2.0 35 115-150 53-88 (118)
272 COG5487 Small integral membran 26.0 1.1E+02 0.0024 18.7 3.0 13 176-188 31-43 (54)
273 PF13963 Transpos_assoc: Trans 25.8 1.3E+02 0.0027 19.9 3.6 38 20-57 11-50 (77)
274 PF14205 Cys_rich_KTR: Cystein 25.7 73 0.0016 19.9 2.2 31 43-78 3-37 (55)
275 COG2824 PhnA Uncharacterized Z 25.7 58 0.0013 23.2 2.0 26 117-143 4-30 (112)
276 PF03833 PolC_DP2: DNA polymer 25.6 23 0.0005 34.3 0.0 38 115-159 654-697 (900)
277 PF08646 Rep_fac-A_C: Replicat 25.3 55 0.0012 24.2 2.0 26 116-142 18-46 (146)
278 KOG2691 RNA polymerase II subu 25.1 69 0.0015 22.9 2.3 33 43-78 3-35 (113)
279 COG3024 Uncharacterized protei 25.1 38 0.00082 21.8 0.9 17 115-131 6-22 (65)
280 PHA03164 hypothetical protein; 24.9 86 0.0019 20.9 2.6 19 179-197 63-81 (88)
281 COG0375 HybF Zn finger protein 24.8 1.3E+02 0.0028 21.8 3.7 47 22-77 39-94 (115)
282 PF04639 Baculo_E56: Baculovir 24.4 56 0.0012 27.6 2.0 18 185-202 285-302 (305)
283 KOG2932 E3 ubiquitin ligase in 24.4 17 0.00037 31.0 -1.0 17 116-132 123-139 (389)
284 PF04695 Pex14_N: Peroxisomal 24.4 25 0.00054 26.1 0.0 23 180-202 110-132 (136)
285 PF14018 DUF4234: Domain of un 24.3 1.1E+02 0.0024 19.8 3.2 19 181-199 6-24 (75)
286 TIGR01195 oadG_fam sodium pump 24.2 1.8E+02 0.0039 19.5 4.2 26 175-200 10-35 (82)
287 smart00336 BBOX B-Box-type zin 24.1 69 0.0015 17.7 1.9 24 67-90 13-36 (42)
288 PF08209 Sgf11: Sgf11 (transcr 24.1 43 0.00094 18.5 0.9 13 117-129 5-17 (33)
289 PHA01399 membrane protein P6 24.0 97 0.0021 24.6 3.1 25 176-200 59-83 (242)
290 PF15135 UPF0515: Uncharacteri 24.0 45 0.00097 27.6 1.4 37 116-152 132-185 (278)
291 PF06682 DUF1183: Protein of u 24.0 75 0.0016 27.3 2.8 16 181-196 162-177 (318)
292 PF15128 T_cell_tran_alt: T-ce 24.0 1.7E+02 0.0036 20.0 3.9 19 170-189 24-42 (92)
293 cd04476 RPA1_DBD_C RPA1_DBD_C: 23.9 51 0.0011 25.0 1.6 26 116-142 34-60 (166)
294 PF13150 DUF3989: Protein of u 23.7 1.7E+02 0.0037 19.9 4.0 16 170-185 27-42 (85)
295 KOG1307 K+-dependent Ca2+/Na+ 23.6 97 0.0021 28.2 3.4 28 174-201 169-204 (588)
296 PF15145 DUF4577: Domain of un 23.3 92 0.002 22.4 2.7 16 185-200 73-88 (128)
297 COG5432 RAD18 RING-finger-cont 22.9 25 0.00055 29.7 -0.3 29 117-152 26-56 (391)
298 PF13894 zf-C2H2_4: C2H2-type 22.9 46 0.00099 15.6 0.8 8 71-78 2-9 (24)
299 PF03884 DUF329: Domain of unk 22.7 34 0.00074 21.5 0.4 14 117-130 3-16 (57)
300 TIGR02605 CxxC_CxxC_SSSS putat 22.6 91 0.002 18.5 2.3 28 46-77 7-34 (52)
301 PF10883 DUF2681: Protein of u 22.5 1.4E+02 0.003 20.5 3.3 13 179-191 10-22 (87)
302 PF02009 Rifin_STEVOR: Rifin/s 22.3 1.2E+02 0.0026 25.8 3.7 23 177-199 258-280 (299)
303 PRK14762 membrane protein; Pro 22.2 1.3E+02 0.0029 15.5 3.2 6 190-195 18-23 (27)
304 PF02701 zf-Dof: Dof domain, z 22.2 22 0.00047 22.8 -0.6 40 115-154 4-43 (63)
305 PF12861 zf-Apc11: Anaphase-pr 22.2 32 0.0007 23.5 0.2 35 117-154 33-67 (85)
306 PF07234 DUF1426: Protein of u 21.9 1.1E+02 0.0023 21.6 2.7 14 174-187 22-35 (117)
307 PRK13454 F0F1 ATP synthase sub 21.9 1.2E+02 0.0027 23.5 3.5 17 177-193 38-54 (181)
308 PTZ00368 universal minicircle 21.9 1.4E+02 0.0031 22.0 3.8 17 79-95 54-70 (148)
309 COG3357 Predicted transcriptio 21.8 1.8E+02 0.0039 20.2 3.8 15 11-25 17-31 (97)
310 PF03811 Zn_Tnp_IS1: InsA N-te 21.6 1.2E+02 0.0025 17.1 2.4 30 44-76 5-36 (36)
311 PF09451 ATG27: Autophagy-rela 20.9 96 0.0021 25.7 2.8 13 67-80 64-76 (268)
312 PF12675 DUF3795: Protein of u 20.8 99 0.0021 20.4 2.4 36 114-149 32-71 (78)
313 PF06682 DUF1183: Protein of u 20.7 89 0.0019 26.8 2.6 19 181-199 159-177 (318)
314 KOG4218 Nuclear hormone recept 20.7 41 0.00088 29.2 0.5 9 116-124 67-75 (475)
315 PRK11088 rrmA 23S rRNA methylt 20.7 63 0.0014 26.5 1.7 25 117-143 3-27 (272)
316 PF15168 TRIQK: Triple QxxK/R 20.6 1.7E+02 0.0038 19.5 3.3 9 189-197 63-71 (79)
317 PF07123 PsbW: Photosystem II 20.4 1E+02 0.0022 23.0 2.5 19 177-195 104-124 (138)
318 PF12113 SVM_signal: SVM prote 20.2 1E+02 0.0022 17.1 1.9 11 177-187 12-22 (33)
319 PF13214 DUF4022: Protein of u 20.2 2E+02 0.0044 18.7 3.5 17 183-199 63-79 (83)
320 PF11375 DUF3177: Protein of u 20.2 90 0.0019 24.6 2.3 14 185-198 165-178 (190)
321 KOG2807 RNA polymerase II tran 20.0 36 0.00078 29.3 0.1 26 66-91 342-367 (378)
322 PF15106 TMEM156: TMEM156 prot 20.0 1.8E+02 0.0038 23.5 3.9 27 167-195 172-198 (226)
323 TIGR00327 secE_euk_arch protei 20.0 2.5E+02 0.0054 17.9 4.3 23 178-200 36-58 (61)
No 1
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=4.4e-32 Score=234.19 Aligned_cols=154 Identities=34% Similarity=0.720 Sum_probs=133.5
Q ss_pred ccCCcccCCCcCCHHHHhhcCCHHHHHHHHHHHHHhhccCCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccc
Q 043865 2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCF 81 (203)
Q Consensus 2 I~CP~~~C~~~l~~~~i~~~l~~e~~~~y~~~~~~~~i~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 81 (203)
|+||..+|+..++.++...+|++++.++|++++.+.+++..+.+|||+|+|...+......+........|+.|+..||.
T Consensus 191 ~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv 270 (384)
T KOG1812|consen 191 IRCPHDGCESRLTLESCRKLLTPKLREMWEQRLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCV 270 (384)
T ss_pred ccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceee
Confidence 78999999999999999999999999999999999999855555999999999887655422234667789999999999
Q ss_pred cCCcCCCCCCccccccccccc--hhHHHHHHHHhccCCCCCCCCceeEecCCcceeEecccccccccccccCcCCCC
Q 043865 82 QCKVAWHAGYRCEESGNLRDW--NDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASG 156 (203)
Q Consensus 82 ~C~~~~H~~~~C~~~~~~~~~--~d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~~~~ 156 (203)
+|+.+||++.+|++++++..+ .|...++++. ++|++||+|+..||+++|||||+|+||++|||.|+.+|..+++
T Consensus 271 ~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la-~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 271 KCKVPWHANLSCEEYKKLNPEEYVDDITLKYLA-KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred cCCCcCCCCCCHHHHHHhCCcccccHHHHHHHH-HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCc
Confidence 999999999999999998743 3334444443 8999999999999999999999999999999999999987654
No 2
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.4e-31 Score=225.22 Aligned_cols=167 Identities=25% Similarity=0.498 Sum_probs=142.4
Q ss_pred CccCCcccCCCcCCHHHHhhcCCHHHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 1 KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 1 ~I~CP~~~C~~~l~~~~i~~~l~~e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
.++||+++|++...+..++++|+.|+++||++.+.+.++. ..+.+|||++.|..+...++. ...+.|.+|+..|
T Consensus 229 ~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~-----~~l~~CskCnFaF 303 (445)
T KOG1814|consen 229 CLKCPDPKCGSVAPPGQVKELVGDELFARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPG-----RALAICSKCNFAF 303 (445)
T ss_pred eecCCCCCCcccCCchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCChhhccCccccCch-----hhhhhhccCccHH
Confidence 4799999999999999999999999999999999999996 899999999999999855554 8899999999999
Q ss_pred cccCCcCCCCCCccccccc--------cccc---------------------hhHHHHHHHHhccCCCCCCCCceeEecC
Q 043865 80 CFQCKVAWHAGYRCEESGN--------LRDW---------------------NDIAFGKLVERMHGARRPACGSCVERKE 130 (203)
Q Consensus 80 C~~C~~~~H~~~~C~~~~~--------~~~~---------------------~d~~~~~~~~~~~~k~CP~C~~~iek~~ 130 (203)
|+.|+..||++..|.--.. +.+. +|.+..+|. ..+.|+||+|.+.|||++
T Consensus 304 CtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl-~~N~krCP~C~v~IEr~e 382 (445)
T KOG1814|consen 304 CTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWL-ESNSKRCPKCKVVIERSE 382 (445)
T ss_pred HHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHH-HhcCCCCCcccceeecCC
Confidence 9999999999888974321 1110 111111222 346799999999999999
Q ss_pred CcceeEe-cccccccccccccCcCCCCCCCCcCCcccchhhHHH
Q 043865 131 GCRVMYC-RCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAI 173 (203)
Q Consensus 131 GCnhm~C-~C~~~FC~~C~~~~~~~~~C~~~~~~~~~~~~~~~~ 173 (203)
|||+|+| .|++.|||.|+....+.+++.|+..+.+.|..+.+.
T Consensus 383 GCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s~c~~~~~~ 426 (445)
T KOG1814|consen 383 GCNKMHCTKCGTYFCWICAELLYPENPYKHFSEPGSECYGQFFG 426 (445)
T ss_pred CccceeeccccccceeehhhhcCCCChhhhhcCCcCccccchhh
Confidence 9999999 899999999999999988999999999999887655
No 3
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=2e-24 Score=176.88 Aligned_cols=144 Identities=25% Similarity=0.562 Sum_probs=116.5
Q ss_pred ccCCcccCCC-cCCHHHHhhcCCHHHHHHHHHHHHHhhccCCCceeCCCCCCCceeeecCccccCCCCceeCCC-ccccc
Q 043865 2 IECPGVHCDQ-FLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPN-CKQWF 79 (203)
Q Consensus 2 I~CP~~~C~~-~l~~~~i~~~l~~e~~~~y~~~~~~~~i~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~-C~~~~ 79 (203)
+-||. +|.. .|..-+..++|+.+.|.+|+++.+|..+...+.+-||+|+|+..+.++++ ..+++|+. |++.|
T Consensus 273 lpc~a-gc~~s~i~e~HHF~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD-----~rkvtC~~gCgf~F 346 (446)
T KOG0006|consen 273 LPCVA-GCPNSLIKELHHFRILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPD-----QRKVTCEGGCGFAF 346 (446)
T ss_pred ccccC-CCchHHHHhhhhheecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCC-----CCcccCCCCchhHh
Confidence 45776 7875 55555667899999999999999999998778999999999999999887 88999997 99999
Q ss_pred cccCCcCCCCCCcccccc--------ccccch--------hHHHHHHHHhccCCCCCCCCceeEecCCcceeEe-c--cc
Q 043865 80 CFQCKVAWHAGYRCEESG--------NLRDWN--------DIAFGKLVERMHGARRPACGSCVERKEGCRVMYC-R--CK 140 (203)
Q Consensus 80 C~~C~~~~H~~~~C~~~~--------~~~~~~--------d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~--C~ 140 (203)
|.+|+..+|.|. |.+.- .+.-++ |+..++.+ +..+|+||+|.++.||++||.||.| + ||
T Consensus 347 CR~C~e~yh~ge-C~~~~~as~t~tc~y~vde~~a~~arwd~as~~TI-k~tTkpCPkChvptErnGGCmHm~Ct~~~Cg 424 (446)
T KOG0006|consen 347 CRECKEAYHEGE-CSAVFEASGTTTCAYRVDERAAEQARWDAASKETI-KKTTKPCPKCHVPTERNGGCMHMKCTQPQCG 424 (446)
T ss_pred HHHHHhhhcccc-ceeeeccccccceeeecChhhhhhhhhhhhhhhhh-hhccCCCCCccCccccCCceEEeecCCCCCC
Confidence 999999999984 55211 111111 22222222 3567999999999999999999999 4 99
Q ss_pred ccccccccccCcC
Q 043865 141 TSFCYECGGNLKS 153 (203)
Q Consensus 141 ~~FC~~C~~~~~~ 153 (203)
.+|||.|+.+|+.
T Consensus 425 ~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 425 LEWCWNCGTEWNR 437 (446)
T ss_pred ceeEeccCChhhh
Confidence 9999999999996
No 4
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.89 E-value=6e-24 Score=187.61 Aligned_cols=158 Identities=23% Similarity=0.468 Sum_probs=131.7
Q ss_pred ccCCcccCCCcCCHHHHhhcCCH-HHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 2 IECPGVHCDQFLDLFTCKLMIPS-NLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 2 I~CP~~~C~~~l~~~~i~~~l~~-e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
|+||..+|.+.++.+++..++++ +..++|.+.+.++++. .....|||+|+|+..+.... .....+.|. |++.|
T Consensus 114 i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~~----~~~~~v~C~-~g~~F 188 (444)
T KOG1815|consen 114 IKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFGS----LESVEVDCG-CGHEF 188 (444)
T ss_pred ccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeeccC----CCccceeCC-CCchh
Confidence 78999999999999999999998 5999999999999997 55689999999999887632 136789995 67799
Q ss_pred cccCCcCCCCCCccccccccccch--hHHHHHHHHhccCCCCCCCCceeEecCCcceeEe-c--ccccccccccccCcCC
Q 043865 80 CFQCKVAWHAGYRCEESGNLRDWN--DIAFGKLVERMHGARRPACGSCVERKEGCRVMYC-R--CKTSFCYECGGNLKSA 154 (203)
Q Consensus 80 C~~C~~~~H~~~~C~~~~~~~~~~--d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~--C~~~FC~~C~~~~~~~ 154 (203)
|+.|+.+||++.+|.....|.... +....+|+ ..++++||+|..+|||++|||||+| . |+++|||.|++.|..|
T Consensus 189 C~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi-~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h 267 (444)
T KOG1815|consen 189 CFACGEESHSPVSCPGAKKWLKKCRDDSETINWI-LANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH 267 (444)
T ss_pred HhhccccccCCCcccchHHHHHhhhhhhhhhhhh-hccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence 999999999999999988876442 22223355 4677899999999999999999999 4 9999999999999998
Q ss_pred C-----CCCCCcCCcc
Q 043865 155 S-----GCLCKEKGDV 165 (203)
Q Consensus 155 ~-----~C~~~~~~~~ 165 (203)
+ .|..+..+..
T Consensus 268 ~~~~~~~c~~~~~~~~ 283 (444)
T KOG1815|consen 268 GSSTGYSCNRYVDGKS 283 (444)
T ss_pred cccceeeeeeeechhh
Confidence 4 4555555443
No 5
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.48 E-value=6.4e-14 Score=91.30 Aligned_cols=63 Identities=35% Similarity=0.847 Sum_probs=55.8
Q ss_pred HHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCCCCCCcc
Q 043865 28 SKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRC 93 (203)
Q Consensus 28 ~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 93 (203)
++|++++.+.+++ +++++|||+|+|+.++..++. .....+.|+.|+..||+.|+.+||++.+|
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~---~~~~~v~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEE---EGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCC---CCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence 4799999999997 689999999999999988642 24788999999999999999999999987
No 6
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.46 E-value=1.3e-14 Score=94.56 Aligned_cols=63 Identities=29% Similarity=0.769 Sum_probs=42.4
Q ss_pred HHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCCCCCCcc
Q 043865 28 SKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRC 93 (203)
Q Consensus 28 ~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C 93 (203)
|||++++++.++. +++++|||+|+|+.++..++. .....++|+.|++.||+.|+.+||+|.+|
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~fC~~C~~~~H~~~~C 64 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDG---CNSPIVTCPSCGTEFCFKCGEPWHEGVTC 64 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SS---TTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCC---CCCCeeECCCCCCcCccccCcccCCCCCC
Confidence 5788899999886 778899999999999998876 11224999999999999999999999887
No 7
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=98.68 E-value=3.7e-08 Score=63.80 Aligned_cols=50 Identities=28% Similarity=0.636 Sum_probs=41.6
Q ss_pred HHHHHHHHh-ccCCCCC--CCCceeEecC--CcceeEe-cccccccccccccCcCC
Q 043865 105 IAFGKLVER-MHGARRP--ACGSCVERKE--GCRVMYC-RCKTSFCYECGGNLKSA 154 (203)
Q Consensus 105 ~~~~~~~~~-~~~k~CP--~C~~~iek~~--GCnhm~C-~C~~~FC~~C~~~~~~~ 154 (203)
..++.+++. .+++.|| +|+..|+..+ |..+|+| .|++.|||.|+.+|...
T Consensus 6 ~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~ 61 (64)
T smart00647 6 LLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSP 61 (64)
T ss_pred HHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCC
Confidence 344555544 5788999 9999999975 9999999 89999999999999754
No 8
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=98.47 E-value=4.2e-08 Score=63.48 Aligned_cols=41 Identities=29% Similarity=0.819 Sum_probs=29.9
Q ss_pred ccCCCCCC--CCceeEecCCcce--eEe-cccccccccccccCcCC
Q 043865 114 MHGARRPA--CGSCVERKEGCRV--MYC-RCKTSFCYECGGNLKSA 154 (203)
Q Consensus 114 ~~~k~CP~--C~~~iek~~GCnh--m~C-~C~~~FC~~C~~~~~~~ 154 (203)
...+.||+ |+..+++.+|.++ |+| .|+++|||.|+.+|...
T Consensus 16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~ 61 (64)
T PF01485_consen 16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEG 61 (64)
T ss_dssp --CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTT
T ss_pred CCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCC
Confidence 45689988 9999999999999 999 59999999999999653
No 9
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.76 E-value=0.0023 Score=55.42 Aligned_cols=46 Identities=26% Similarity=0.545 Sum_probs=41.0
Q ss_pred cCCCCCC--CCceeEecCCcceeEe-cccccccccccccCcCCCCCCCC
Q 043865 115 HGARRPA--CGSCVERKEGCRVMYC-RCKTSFCYECGGNLKSASGCLCK 160 (203)
Q Consensus 115 ~~k~CP~--C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~~~~C~~~ 160 (203)
.+.-||+ |+.++-.+.|..-..| .|...||.+|...|....+|.-.
T Consensus 272 dv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~ 320 (445)
T KOG1814|consen 272 DVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVK 320 (445)
T ss_pred ccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcCCCcccCc
Confidence 5689998 9999977899999999 89999999999999987767665
No 10
>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=95.17 E-value=0.0087 Score=31.64 Aligned_cols=23 Identities=30% Similarity=0.816 Sum_probs=15.0
Q ss_pred CCCCCCCceeEecCCcceeEe-cccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
|.||.|+..|..+ -..| .|||.|
T Consensus 1 K~CP~C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPECGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCCCcCCchhh----cCcCCCCCCCC
Confidence 5788888888432 3556 466665
No 11
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.24 E-value=0.031 Score=48.91 Aligned_cols=43 Identities=21% Similarity=0.624 Sum_probs=36.0
Q ss_pred CCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCCCCCCc
Q 043865 42 FERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYR 92 (203)
Q Consensus 42 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~ 92 (203)
..++.|| .|+..+..... ...++|. |++.||+.|..+|+.+..
T Consensus 304 ~~wr~Cp--kC~~~ie~~~G-----Cnhm~Cr-C~~~fcy~C~~~~~~~~~ 346 (384)
T KOG1812|consen 304 KRWRQCP--KCKFMIELSEG-----CNHMTCR-CGHQFCYMCGGDWKTHNG 346 (384)
T ss_pred HhcCcCc--ccceeeeecCC-----cceEEee-ccccchhhcCcchhhCCc
Confidence 5688999 69988866554 8999998 999999999999966554
No 12
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.32 E-value=0.087 Score=30.18 Aligned_cols=33 Identities=30% Similarity=0.681 Sum_probs=24.0
Q ss_pred ceeCCCCCCCceeeecCc-cccCCCCceeCCCccccc
Q 043865 44 RSYCPNRNCMALVVNEGE-INYGTLKKARCPNCKQWF 79 (203)
Q Consensus 44 ~~~Cp~~~C~~~~~~~~~-~~~~~~~~~~C~~C~~~~ 79 (203)
.+.|| +|+..+..++. ++ .+...++|+.|++.|
T Consensus 2 ~i~CP--~C~~~f~v~~~~l~-~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCP--NCQTRFRVPDDKLP-AGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECC--CCCceEEcCHHHcc-cCCcEEECCCCCcEe
Confidence 46788 59988876554 33 346699999999875
No 13
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.82 E-value=0.12 Score=29.44 Aligned_cols=33 Identities=36% Similarity=0.655 Sum_probs=23.8
Q ss_pred ceeCCCCCCCceeeecCc-cccCCCCceeCCCccccc
Q 043865 44 RSYCPNRNCMALVVNEGE-INYGTLKKARCPNCKQWF 79 (203)
Q Consensus 44 ~~~Cp~~~C~~~~~~~~~-~~~~~~~~~~C~~C~~~~ 79 (203)
.+.|| +|+..+..++. ++ .....++|+.|++.|
T Consensus 2 ~i~Cp--~C~~~y~i~d~~ip-~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCP--NCQAKYEIDDEKIP-PKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECC--CCCCEEeCCHHHCC-CCCcEEECCCCCCEe
Confidence 46788 59988766554 44 346689999999875
No 14
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.48 E-value=0.097 Score=46.72 Aligned_cols=45 Identities=27% Similarity=0.584 Sum_probs=37.5
Q ss_pred CCCCC--CCCceeEe-cCCcceeEecccccccccccccCcCCCCCCCC
Q 043865 116 GARRP--ACGSCVER-KEGCRVMYCRCKTSFCYECGGNLKSASGCLCK 160 (203)
Q Consensus 116 ~k~CP--~C~~~iek-~~GCnhm~C~C~~~FC~~C~~~~~~~~~C~~~ 160 (203)
.+-|| .|+..+.. .+....+.|.|++.|||.|+.+|.....|+..
T Consensus 158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~ 205 (444)
T KOG1815|consen 158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGA 205 (444)
T ss_pred cccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccch
Confidence 45565 79999988 78899999999999999999999986655543
No 15
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=92.20 E-value=0.11 Score=31.81 Aligned_cols=27 Identities=33% Similarity=0.624 Sum_probs=20.7
Q ss_pred CCCCCCCceeEecCC--cceeEe-cccccc
Q 043865 117 ARRPACGSCVERKEG--CRVMYC-RCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~~G--Cnhm~C-~C~~~F 143 (203)
+.||.|+.++...++ -++..| .||+++
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 469999998877644 468899 699764
No 16
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=91.98 E-value=0.075 Score=27.93 Aligned_cols=23 Identities=30% Similarity=0.858 Sum_probs=14.5
Q ss_pred CCCCCCCceeEecCCcceeEeccccccccccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYCRCKTSFCYECGGN 150 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~ 150 (203)
+.||+|+..++.. ..||-.||++
T Consensus 3 ~~Cp~Cg~~~~~~-----------~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPD-----------AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcc-----------cccChhhCCC
Confidence 5688888866442 4566666654
No 17
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=91.76 E-value=0.21 Score=31.75 Aligned_cols=26 Identities=27% Similarity=0.722 Sum_probs=19.1
Q ss_pred CCCCCCCceeEecCCcceeEecccccccc-cccccCcC
Q 043865 117 ARRPACGSCVERKEGCRVMYCRCKTSFCY-ECGGNLKS 153 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C~C~~~FC~-~C~~~~~~ 153 (203)
|.||.||.+|.- ...||. .|++.|..
T Consensus 4 kHC~~CG~~Ip~-----------~~~fCS~~C~~~~~k 30 (59)
T PF09889_consen 4 KHCPVCGKPIPP-----------DESFCSPKCREEYRK 30 (59)
T ss_pred CcCCcCCCcCCc-----------chhhhCHHHHHHHHH
Confidence 678888888874 357774 77777774
No 18
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=91.51 E-value=0.084 Score=26.98 Aligned_cols=11 Identities=36% Similarity=0.785 Sum_probs=7.2
Q ss_pred CCCCCCceeEe
Q 043865 118 RRPACGSCVER 128 (203)
Q Consensus 118 ~CP~C~~~iek 128 (203)
.||+|+..|+.
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 37777777754
No 19
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=91.19 E-value=0.14 Score=31.49 Aligned_cols=27 Identities=22% Similarity=0.449 Sum_probs=20.0
Q ss_pred cCCCCCCCCc-eeEecCCcceeEe-cccccc
Q 043865 115 HGARRPACGS-CVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 115 ~~k~CP~C~~-~iek~~GCnhm~C-~C~~~F 143 (203)
..+.||+|+. ...... +.++| +||+.+
T Consensus 19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE 47 (50)
T ss_pred ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence 3468999998 444434 79999 799865
No 20
>PHA00626 hypothetical protein
Probab=90.85 E-value=0.19 Score=31.43 Aligned_cols=26 Identities=27% Similarity=0.586 Sum_probs=19.4
Q ss_pred CCCCCCc-eeEecCCcce----eEe-cccccc
Q 043865 118 RRPACGS-CVERKEGCRV----MYC-RCKTSF 143 (203)
Q Consensus 118 ~CP~C~~-~iek~~GCnh----m~C-~C~~~F 143 (203)
.||+|+. .|.|.+-|+. ..| .||+.|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 5999999 5778766544 678 688776
No 21
>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=90.65 E-value=0.29 Score=27.90 Aligned_cols=32 Identities=25% Similarity=0.545 Sum_probs=21.4
Q ss_pred eeCCCCCCCceeeecCc-cccCCCCceeCCCccccc
Q 043865 45 SYCPNRNCMALVVNEGE-INYGTLKKARCPNCKQWF 79 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~-~~~~~~~~~~C~~C~~~~ 79 (203)
+.|| +|+..+..++. +. +....+.||.|++.|
T Consensus 3 ~~CP--~C~~~~~v~~~~~~-~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCP--NCKTSFRVVDSQLG-ANGGKVRCGKCGHVW 35 (38)
T ss_pred EECC--CCCCEEEeCHHHcC-CCCCEEECCCCCCEE
Confidence 5688 59987765543 22 223479999998764
No 22
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.44 E-value=0.24 Score=29.65 Aligned_cols=29 Identities=24% Similarity=0.400 Sum_probs=20.1
Q ss_pred CCCCCCCceeEecCCcceeEe-cccccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSFCY 145 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~FC~ 145 (203)
-+||+|+..++..++=..++| .||..+=+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 358888888877755557788 58776543
No 23
>PLN03086 PRLI-interacting factor K; Provisional
Probab=89.75 E-value=0.65 Score=42.62 Aligned_cols=56 Identities=23% Similarity=0.565 Sum_probs=33.7
Q ss_pred ccCCcccCCCcCCHHHHhhcCCHHHHHHHHHHHHHhhccCCCceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 2 I~CP~~~C~~~l~~~~i~~~l~~e~~~~y~~~~~~~~i~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
+.||. |+..+....+...+. +- .-+.+-||+.+|+..+..... .....|+.|+..|
T Consensus 408 V~C~N--C~~~i~l~~l~lHe~--------------~C-~r~~V~Cp~~~Cg~v~~r~el-----~~H~~C~~Cgk~f 463 (567)
T PLN03086 408 VECRN--CKHYIPSRSIALHEA--------------YC-SRHNVVCPHDGCGIVLRVEEA-----KNHVHCEKCGQAF 463 (567)
T ss_pred EECCC--CCCccchhHHHHHHh--------------hC-CCcceeCCcccccceeecccc-----ccCccCCCCCCcc
Confidence 45774 777776655543221 00 124567887678888765544 4556788887765
No 24
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=88.71 E-value=0.28 Score=29.87 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=21.1
Q ss_pred cCCCCCCCCceeEecCCcceeEe-cccc
Q 043865 115 HGARRPACGSCVERKEGCRVMYC-RCKT 141 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C-~C~~ 141 (203)
.-+.||+|+.-+...+-=+...| +||+
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccc
Confidence 34789999977766666668899 8986
No 25
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=88.43 E-value=0.57 Score=25.72 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=17.2
Q ss_pred CCCCCCCCceeEecCCcceeEe-ccccc
Q 043865 116 GARRPACGSCVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 142 (203)
.+-||+|+.+.+...+=-.|.| .|+.+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCE
Confidence 4779999999999888778888 68865
No 26
>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=86.36 E-value=0.27 Score=30.31 Aligned_cols=25 Identities=40% Similarity=0.990 Sum_probs=16.0
Q ss_pred CCceeCCCccccccccCCcCCCCCC
Q 043865 67 LKKARCPNCKQWFCFQCKVAWHAGY 91 (203)
Q Consensus 67 ~~~~~C~~C~~~~C~~C~~~~H~~~ 91 (203)
....+||.|++.||..|-.-.|+.+
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~L 43 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETL 43 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS
T ss_pred CCeEECCCCCCccccCcChhhhccc
Confidence 5679999999999999988778754
No 27
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=85.22 E-value=0.71 Score=32.29 Aligned_cols=29 Identities=28% Similarity=0.637 Sum_probs=22.2
Q ss_pred CCCCCCceeEec--CCcceeEe-ccccccccc
Q 043865 118 RRPACGSCVERK--EGCRVMYC-RCKTSFCYE 146 (203)
Q Consensus 118 ~CP~C~~~iek~--~GCnhm~C-~C~~~FC~~ 146 (203)
.||.|+.+..-. +.||...| .|.|.|=-.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence 599999865544 44999999 699987543
No 28
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=84.80 E-value=0.66 Score=26.19 Aligned_cols=28 Identities=25% Similarity=0.673 Sum_probs=18.0
Q ss_pred eeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
++|| .|++.+.+... . .....|+.|++.
T Consensus 2 ~FCp--~C~nlL~p~~~---~-~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 2 RFCP--ECGNLLYPKED---K-EKRVACRTCGYE 29 (35)
T ss_dssp -BET--TTTSBEEEEEE---T-TTTEEESSSS-E
T ss_pred eeCC--CCCccceEcCC---C-ccCcCCCCCCCc
Confidence 5788 69999987665 1 222278888764
No 29
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=84.55 E-value=0.84 Score=27.70 Aligned_cols=28 Identities=18% Similarity=0.628 Sum_probs=19.2
Q ss_pred eCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 46 YCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 46 ~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
+|| .|+..+..... +......|+.|++.
T Consensus 2 FCp--~Cg~~l~~~~~---~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCP--KCGNMLIPKEG---KEKRRFVCRKCGYE 29 (52)
T ss_pred CCC--CCCCccccccC---CCCCEEECCcCCCe
Confidence 687 69998876543 12247889988864
No 30
>PHA03049 IMV membrane protein; Provisional
Probab=83.81 E-value=1.6 Score=28.18 Aligned_cols=22 Identities=32% Similarity=0.788 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 043865 175 SGLILIFTVLGVLGGVIYGIYC 196 (203)
Q Consensus 175 ~~~~~~f~~l~~~~~~~~~~~~ 196 (203)
.-++|+-+-..++|+++|++|=
T Consensus 3 ~d~~l~iICVaIi~lIvYgiYn 24 (68)
T PHA03049 3 GDIILVIICVVIIGLIVYGIYN 24 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3356666677888899999994
No 31
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=82.77 E-value=1.9 Score=25.61 Aligned_cols=29 Identities=24% Similarity=0.393 Sum_probs=21.3
Q ss_pred eeCCCCCCCceeeecCccccCCCCceeCCCcccccc
Q 043865 45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFC 80 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C 80 (203)
..|| +|+..+..++. ...+.||.||..+=
T Consensus 4 y~C~--~CG~~~~~~~~-----~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCA--RCGREVELDEY-----GTGVRCPYCGYRIL 32 (46)
T ss_pred EECC--CCCCEEEECCC-----CCceECCCCCCeEE
Confidence 4677 69998877665 33789999987643
No 32
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=82.21 E-value=1.1 Score=27.05 Aligned_cols=30 Identities=27% Similarity=0.484 Sum_probs=20.2
Q ss_pred CceeCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 43 ERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 43 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
....||++.|+..+..... .....|.+|+.
T Consensus 17 ~rk~CP~~~CG~GvFMA~H-----~dR~~CGKCg~ 46 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEH-----KDRHYCGKCGY 46 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE------SSEEEETTTSS
T ss_pred hhhcCCCcccCCceEeeec-----CCCccCCCccc
Confidence 3689999999986554444 45778877764
No 33
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=81.84 E-value=1.1 Score=28.47 Aligned_cols=33 Identities=24% Similarity=0.598 Sum_probs=21.6
Q ss_pred eeCCCCCCCceeeecCccccCCCCceeCCCccccccccCC
Q 043865 45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCK 84 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~ 84 (203)
-.|. +|+..+.+... ...+.||.|+...=.+|.
T Consensus 10 ~~Ct--SCg~~i~p~e~-----~v~F~CPnCGe~~I~Rc~ 42 (61)
T COG2888 10 PVCT--SCGREIAPGET-----AVKFPCPNCGEVEIYRCA 42 (61)
T ss_pred ceec--cCCCEeccCCc-----eeEeeCCCCCceeeehhh
Confidence 3455 47777644443 678999999976654444
No 34
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=81.76 E-value=1.3 Score=37.60 Aligned_cols=40 Identities=23% Similarity=0.757 Sum_probs=31.1
Q ss_pred CceeCCCCCCCceeeecCccccCCCCceeCCC--ccccccccCCcCCCC
Q 043865 43 ERSYCPNRNCMALVVNEGEINYGTLKKARCPN--CKQWFCFQCKVAWHA 89 (203)
Q Consensus 43 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~ 89 (203)
....|| .|......++. .-.+.|+. |+..+|++|+.+|..
T Consensus 396 tTkpCP--kChvptErnGG-----CmHm~Ct~~~Cg~eWCw~C~tEW~r 437 (446)
T KOG0006|consen 396 TTKPCP--KCHVPTERNGG-----CMHMKCTQPQCGLEWCWNCGTEWNR 437 (446)
T ss_pred ccCCCC--CccCccccCCc-----eEEeecCCCCCCceeEeccCChhhh
Confidence 445566 68877666554 77889976 999999999999965
No 35
>PF05961 Chordopox_A13L: Chordopoxvirus A13L protein; InterPro: IPR009236 This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus [].
Probab=81.56 E-value=2.2 Score=27.66 Aligned_cols=24 Identities=33% Similarity=0.715 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhh
Q 043865 175 SGLILIFTVLGVLGGVIYGIYCVI 198 (203)
Q Consensus 175 ~~~~~~f~~l~~~~~~~~~~~~~~ 198 (203)
.-++|+-+=..++|+++|++|==.
T Consensus 3 ~d~iLi~ICVaii~lIlY~iYnr~ 26 (68)
T PF05961_consen 3 GDFILIIICVAIIGLILYGIYNRK 26 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 335666677788889999999533
No 36
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=80.76 E-value=11 Score=31.13 Aligned_cols=45 Identities=18% Similarity=0.431 Sum_probs=28.7
Q ss_pred CCCCC--CCceeEec--------------CCcceeEe-cccccccccccccCcCCCCCCCCcC
Q 043865 117 ARRPA--CGSCVERK--------------EGCRVMYC-RCKTSFCYECGGNLKSASGCLCKEK 162 (203)
Q Consensus 117 k~CP~--C~~~iek~--------------~GCnhm~C-~C~~~FC~~C~~~~~~~~~C~~~~~ 162 (203)
--||+ |+..|... .|--.++| .|...|=|.=... +....|+|=.+
T Consensus 124 IaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~-~tlARCPHCrK 185 (256)
T PF09788_consen 124 IACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTS-NTLARCPHCRK 185 (256)
T ss_pred ccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCC-CccccCCCCce
Confidence 35875 99988754 24455899 8999999984331 12234665443
No 37
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=80.24 E-value=1.9 Score=23.02 Aligned_cols=20 Identities=40% Similarity=0.718 Sum_probs=13.7
Q ss_pred CCCCCCceeEecCCcceeEe
Q 043865 118 RRPACGSCVERKEGCRVMYC 137 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C 137 (203)
.||.|+..+.+.+|=-..+|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 59999999999998777777
No 38
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=79.94 E-value=0.73 Score=30.84 Aligned_cols=46 Identities=20% Similarity=0.341 Sum_probs=18.3
Q ss_pred CCCCceeCCCccccccccCCcCCCCCCccccccccccchhHHHHHHHHhccCCCCCCCCceeEecCCcce
Q 043865 65 GTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRV 134 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GCnh 134 (203)
++...+.|..|+.-.|.. |-+|.. +.+.+-||+|+....+..|+-.
T Consensus 24 ~Ge~FVAC~eC~fPvCr~----------CyEYEr--------------keg~q~CpqCkt~ykr~kgsp~ 69 (80)
T PF14569_consen 24 NGEVFVACHECAFPVCRP----------CYEYER--------------KEGNQVCPQCKTRYKRHKGSPR 69 (80)
T ss_dssp SSSB--S-SSS-----HH----------HHHHHH--------------HTS-SB-TTT--B----TT---
T ss_pred CCCEEEEEcccCCccchh----------HHHHHh--------------hcCcccccccCCCcccccCCCC
Confidence 356788888888888853 444432 4677899999999988877654
No 39
>PF14353 CpXC: CpXC protein
Probab=79.53 E-value=1.5 Score=32.07 Aligned_cols=27 Identities=15% Similarity=0.306 Sum_probs=16.5
Q ss_pred hhHHHHHHHHh--ccCCCCCCCCceeEec
Q 043865 103 NDIAFGKLVER--MHGARRPACGSCVERK 129 (203)
Q Consensus 103 ~d~~~~~~~~~--~~~k~CP~C~~~iek~ 129 (203)
.+..+++.+-+ -..-.||+|+..+.-.
T Consensus 23 ~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 23 EDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 35555544432 3456899999887644
No 40
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=78.69 E-value=1.9 Score=24.18 Aligned_cols=25 Identities=36% Similarity=0.760 Sum_probs=12.8
Q ss_pred CCCCCCCceeEec--CC--cceeEe-cccc
Q 043865 117 ARRPACGSCVERK--EG--CRVMYC-RCKT 141 (203)
Q Consensus 117 k~CP~C~~~iek~--~G--Cnhm~C-~C~~ 141 (203)
|-||+|+..++.. +| =..+.| .|++
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCC
Confidence 4689999888875 44 444667 5764
No 41
>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=78.57 E-value=1.6 Score=23.76 Aligned_cols=25 Identities=28% Similarity=0.773 Sum_probs=12.4
Q ss_pred CCCCCCceeEecCCcceeEe-cccccc
Q 043865 118 RRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
.||.|+.-..-.+|. .|.| .|+++|
T Consensus 4 ~Cp~C~se~~y~D~~-~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGE-LLVCPECGHEW 29 (30)
T ss_dssp --TTT-----EE-SS-SEEETTTTEEE
T ss_pred CCCCCCCcceeccCC-EEeCCcccccC
Confidence 689999888887775 4668 688765
No 42
>PF09680 Tiny_TM_bacill: Protein of unknown function (Tiny_TM_bacill); InterPro: IPR010070 This entry represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=77.82 E-value=2.3 Score=21.79 Aligned_cols=16 Identities=19% Similarity=0.582 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHHH
Q 043865 174 ISGLILIFTVLGVLGG 189 (203)
Q Consensus 174 ~~~~~~~f~~l~~~~~ 189 (203)
|++++.+|++|.++|.
T Consensus 6 FalivVLFILLiIvG~ 21 (24)
T PF09680_consen 6 FALIVVLFILLIIVGA 21 (24)
T ss_pred chhHHHHHHHHHHhcc
Confidence 3446677888887764
No 43
>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=77.81 E-value=1.7 Score=28.06 Aligned_cols=28 Identities=25% Similarity=0.612 Sum_probs=21.8
Q ss_pred cCCCCCCCCceeEecCCcceeEe-ccccc
Q 043865 115 HGARRPACGSCVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~ 142 (203)
..+.||.|+...++...=..++| .||+.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 45899999999998555567788 58765
No 44
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=77.63 E-value=3.7 Score=30.90 Aligned_cols=36 Identities=19% Similarity=0.309 Sum_probs=22.3
Q ss_pred CCCceeCCCCCCCceeeecCcccc-CCCCceeCCCcccc
Q 043865 41 GFERSYCPNRNCMALVVNEGEINY-GTLKKARCPNCKQW 78 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~~~~~~~~~~-~~~~~~~C~~C~~~ 78 (203)
......|| .|+.-+...+.... +....+.||.||..
T Consensus 96 ~~~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CCcEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 55678898 48877765433111 12344999988764
No 45
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=77.35 E-value=1.4 Score=42.11 Aligned_cols=26 Identities=46% Similarity=1.031 Sum_probs=23.1
Q ss_pred CCCCCCCceeEecCCcceeEe-ccccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSFC 144 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~FC 144 (203)
..||.|+..+...+||. +| .|||.=|
T Consensus 725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~skC 751 (752)
T PRK08665 725 GACPECGSILEHEEGCV--VCHSCGYSKC 751 (752)
T ss_pred CCCCCCCcccEECCCCC--cCCCCCCCCC
Confidence 35999999999999998 99 6999866
No 46
>MTH00261 ATP8 ATP synthase F0 subunit 8; Provisional
Probab=76.86 E-value=4 Score=25.54 Aligned_cols=25 Identities=20% Similarity=0.437 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhh
Q 043865 174 ISGLILIFTVLGVLGGVIYGIYCVI 198 (203)
Q Consensus 174 ~~~~~~~f~~l~~~~~~~~~~~~~~ 198 (203)
|++++++|+++.++++-.|.++++.
T Consensus 14 fvllllf~iliilisikfynfflvl 38 (68)
T MTH00261 14 FVLLLLFFILIILISIKFYNFFLVL 38 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHhheeE
Confidence 4556666666666667788888763
No 47
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=76.60 E-value=0.44 Score=39.75 Aligned_cols=33 Identities=18% Similarity=0.285 Sum_probs=24.1
Q ss_pred CCCCCCCCceeEecCCcceeEe-cccccccccccccCcCC
Q 043865 116 GARRPACGSCVERKEGCRVMYC-RCKTSFCYECGGNLKSA 154 (203)
Q Consensus 116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~~ 154 (203)
..+|--|-...+ |-+| .|||-|||.|...|-..
T Consensus 239 ~~kC~LCLe~~~------~pSaTpCGHiFCWsCI~~w~~e 272 (293)
T KOG0317|consen 239 TRKCSLCLENRS------NPSATPCGHIFCWSCILEWCSE 272 (293)
T ss_pred CCceEEEecCCC------CCCcCcCcchHHHHHHHHHHcc
Confidence 355655554443 6678 79999999999999863
No 48
>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=76.49 E-value=1.4 Score=31.58 Aligned_cols=26 Identities=27% Similarity=0.648 Sum_probs=18.0
Q ss_pred CCCCCCCceeEecCCcceeEe-cccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
|.||+|+...---.- +-++| .||+.|
T Consensus 10 R~Cp~CG~kFYDLnk-~PivCP~CG~~~ 36 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK-DPIVCPKCGTEF 36 (108)
T ss_pred ccCCCCcchhccCCC-CCccCCCCCCcc
Confidence 568888886654444 77788 677765
No 49
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=76.12 E-value=2.3 Score=27.99 Aligned_cols=34 Identities=29% Similarity=0.731 Sum_probs=22.5
Q ss_pred CCCCCCceeEecCCcceeEe-ccccc-----ccccccccCcC
Q 043865 118 RRPACGSCVERKEGCRVMYC-RCKTS-----FCYECGGNLKS 153 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~~~~ 153 (203)
.||.|+..++..+ .+.+| .|+.+ +|-.|++++..
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred cCCCCCCccEEeC--CEEECccccccceecccCCCcccHHHH
Confidence 5999999999888 78999 78854 58899888764
No 50
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.72 E-value=1.3 Score=41.50 Aligned_cols=32 Identities=25% Similarity=0.652 Sum_probs=20.0
Q ss_pred CCCCCCCCceeEecCCcceeEe-ccccc------ccccccccCcC
Q 043865 116 GARRPACGSCVERKEGCRVMYC-RCKTS------FCYECGGNLKS 153 (203)
Q Consensus 116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~------FC~~C~~~~~~ 153 (203)
.|.||+||.... +..| .||+. ||-.||.+..+
T Consensus 15 akFC~~CG~~l~------~~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 15 NRFCQKCGTSLT------HKPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CccccccCCCCC------CCcCCCCCCCCCcccccccccCCcccc
Confidence 355666666552 2356 46544 99999888654
No 51
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=75.30 E-value=1.6 Score=25.89 Aligned_cols=27 Identities=30% Similarity=0.627 Sum_probs=19.6
Q ss_pred hccCCCCCCCCceeEecCCcceeEe---cccccc
Q 043865 113 RMHGARRPACGSCVERKEGCRVMYC---RCKTSF 143 (203)
Q Consensus 113 ~~~~k~CP~C~~~iek~~GCnhm~C---~C~~~F 143 (203)
..+++.||+|++.- |.--+.| .|++.|
T Consensus 8 lRGirkCp~CGt~N----G~R~~~CKN~~C~~~~ 37 (44)
T PF14952_consen 8 LRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF 37 (44)
T ss_pred HhccccCCcCcCcc----CcccccccCCccchhh
Confidence 35789999999876 6666777 266554
No 52
>TIGR02972 TMAO_torE trimethylamine N-oxide reductase system, TorE protein. Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA.
Probab=75.21 E-value=11 Score=22.78 Aligned_cols=30 Identities=23% Similarity=0.277 Sum_probs=19.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043865 168 HHYCAIISGLILIFTVLGVLGGVIYGIYCV 197 (203)
Q Consensus 168 ~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~ 197 (203)
.+..+.+.+..++|.+|++..+-.|++..-
T Consensus 8 ~El~~flfl~v~l~PiLsV~~Vg~YGF~vW 37 (47)
T TIGR02972 8 NELKALGFIIVVLFPILSVAGIGGYGFIIW 37 (47)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555556677788887777777776543
No 53
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.15 E-value=2.2 Score=30.72 Aligned_cols=45 Identities=22% Similarity=0.533 Sum_probs=29.4
Q ss_pred eeCCCCCCCceeeecCcc--c-cCCCCceeCCCccccccccCCcCCCCCC
Q 043865 45 SYCPNRNCMALVVNEGEI--N-YGTLKKARCPNCKQWFCFQCKVAWHAGY 91 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~--~-~~~~~~~~C~~C~~~~C~~C~~~~H~~~ 91 (203)
..|- .|...+...... + .......+|+.|++.||..|..-+|+.+
T Consensus 56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~L 103 (112)
T TIGR00622 56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESL 103 (112)
T ss_pred Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhc
Confidence 3465 577766432110 0 1124578899999999999998888643
No 54
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=75.10 E-value=0.6 Score=36.90 Aligned_cols=35 Identities=17% Similarity=0.279 Sum_probs=24.6
Q ss_pred hccCCCCCCCCceeEecCCcceeEecccccccccccccCc
Q 043865 113 RMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLK 152 (203)
Q Consensus 113 ~~~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~ 152 (203)
..+.-.||-|.-.+.. -+.=.|||.|||.|...|.
T Consensus 15 ~~~~~~CpICld~~~d-----PVvT~CGH~FC~~CI~~wl 49 (193)
T PLN03208 15 SGGDFDCNICLDQVRD-----PVVTLCGHLFCWPCIHKWT 49 (193)
T ss_pred CCCccCCccCCCcCCC-----cEEcCCCchhHHHHHHHHH
Confidence 3445689999876531 1333799999999988773
No 55
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=75.08 E-value=0.56 Score=39.58 Aligned_cols=30 Identities=23% Similarity=0.524 Sum_probs=24.1
Q ss_pred ccCCCCCCCCceeEec-CCcceeEe-cccccc
Q 043865 114 MHGARRPACGSCVERK-EGCRVMYC-RCKTSF 143 (203)
Q Consensus 114 ~~~k~CP~C~~~iek~-~GCnhm~C-~C~~~F 143 (203)
.-|.+||+|+..+.+. -.=|.+.| .|+++|
T Consensus 25 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 25 GLWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CCeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 3589999999988765 34567899 799998
No 56
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=74.93 E-value=2.6 Score=40.07 Aligned_cols=34 Identities=29% Similarity=0.641 Sum_probs=29.9
Q ss_pred CCCCCCCceeEecCCcceeEe-ccccc-----cccccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTS-----FCYECGGN 150 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 150 (203)
-+||+|..+..--..=+.|.| .||++ .|..||..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 389999999888777799999 69987 89999888
No 57
>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=74.86 E-value=1.9 Score=30.28 Aligned_cols=24 Identities=33% Similarity=0.599 Sum_probs=18.3
Q ss_pred CCCCCCceeEecCCcceeEe-cccccc
Q 043865 118 RRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
.||+|+.++...+ +.+.| .|++.+
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYEK 26 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCcc
Confidence 6999999887655 47888 688763
No 58
>TIGR01732 tiny_TM_bacill conserved hypothetical tiny transmembrane protein. This model represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV.
Probab=74.51 E-value=3.8 Score=21.42 Aligned_cols=15 Identities=20% Similarity=0.625 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHH
Q 043865 175 SGLILIFTVLGVLGG 189 (203)
Q Consensus 175 ~~~~~~f~~l~~~~~ 189 (203)
..++.+||+|.++|.
T Consensus 9 ~livVLFILLIIiga 23 (26)
T TIGR01732 9 ALIVVLFILLVIVGA 23 (26)
T ss_pred HHHHHHHHHHHHhhe
Confidence 345677888877763
No 59
>COG4640 Predicted membrane protein [Function unknown]
Probab=73.93 E-value=4.2 Score=35.64 Aligned_cols=23 Identities=17% Similarity=0.148 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 043865 172 AIISGLILIFTVLGVLGGVIYGI 194 (203)
Q Consensus 172 ~~~~~~~~~f~~l~~~~~~~~~~ 194 (203)
++|++..++|+++++++.+.|+-
T Consensus 51 ~ii~was~a~~lIlii~~~~fgk 73 (465)
T COG4640 51 KIIPWASGAFILILIIILFFFGK 73 (465)
T ss_pred eeehhHHHHHHHHHHHHHHHHhh
Confidence 34555555555555554444443
No 60
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=73.33 E-value=3.4 Score=24.19 Aligned_cols=23 Identities=39% Similarity=1.008 Sum_probs=17.2
Q ss_pred CCCCCCCCceeEe-cCCcceeEe-ccc
Q 043865 116 GARRPACGSCVER-KEGCRVMYC-RCK 140 (203)
Q Consensus 116 ~k~CP~C~~~iek-~~GCnhm~C-~C~ 140 (203)
...||.|+.+..+ .+| .+.| .|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDG--KIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCC--CEECCCCC
Confidence 3689999999998 455 5677 563
No 61
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=72.77 E-value=4.4 Score=31.64 Aligned_cols=60 Identities=17% Similarity=0.227 Sum_probs=33.1
Q ss_pred CCHHHHhhcCCHHHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 13 LDLFTCKLMIPSNLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 13 l~~~~i~~~l~~e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
++.+.+...+..+....-++...+.... +..+..||+ |+.-+..++.. ...+.||.||..
T Consensus 85 l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~~Y~Cp~--C~~rytf~eA~----~~~F~Cp~Cg~~ 145 (178)
T PRK06266 85 PELEKLPEIIKKKKMEELKKLKEQLEEEENNMFFFCPN--CHIRFTFDEAM----EYGFRCPQCGEM 145 (178)
T ss_pred eCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCEEECCC--CCcEEeHHHHh----hcCCcCCCCCCC
Confidence 4455555555444433222222222222 567888985 88766655442 456899988764
No 62
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.65 E-value=0.94 Score=36.65 Aligned_cols=16 Identities=25% Similarity=0.607 Sum_probs=14.1
Q ss_pred cccccccccccccCcC
Q 043865 138 RCKTSFCYECGGNLKS 153 (203)
Q Consensus 138 ~C~~~FC~~C~~~~~~ 153 (203)
.|||-|||-|+-.|..
T Consensus 64 lCGHLFCWpClyqWl~ 79 (230)
T KOG0823|consen 64 LCGHLFCWPCLYQWLQ 79 (230)
T ss_pred ecccceehHHHHHHHh
Confidence 4899999999999885
No 63
>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=72.54 E-value=4.2 Score=31.07 Aligned_cols=60 Identities=12% Similarity=0.069 Sum_probs=32.2
Q ss_pred CCHHHHhhcCCHHHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 13 LDLFTCKLMIPSNLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 13 l~~~~i~~~l~~e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
++.+++...+..+..+.-++...+..-. +..+..||+ |+.-+..++.. ...+.||.||..
T Consensus 77 i~~~~i~d~Ik~~~~~~~~~lk~~l~~e~~~~~Y~Cp~--c~~r~tf~eA~----~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 77 INYEKALDVLKRKLEETAKKLREKLEFETNNMFFICPN--MCVRFTFNEAM----ELNFTCPRCGAM 137 (158)
T ss_pred eCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEECCC--CCcEeeHHHHH----HcCCcCCCCCCE
Confidence 3444554444433333222222222222 567888985 87666555442 356899988875
No 64
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=72.45 E-value=0.82 Score=26.10 Aligned_cols=20 Identities=30% Similarity=0.587 Sum_probs=15.6
Q ss_pred eeEe-cccccccccccccCcC
Q 043865 134 VMYC-RCKTSFCYECGGNLKS 153 (203)
Q Consensus 134 hm~C-~C~~~FC~~C~~~~~~ 153 (203)
-+.- .||+.||+.|...|..
T Consensus 11 ~~~~~~CGH~fC~~C~~~~~~ 31 (39)
T PF13923_consen 11 PVVVTPCGHSFCKECIEKYLE 31 (39)
T ss_dssp EEEECTTSEEEEHHHHHHHHH
T ss_pred cCEECCCCCchhHHHHHHHHH
Confidence 3345 7999999999888764
No 65
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=71.99 E-value=1 Score=26.35 Aligned_cols=20 Identities=30% Similarity=0.532 Sum_probs=16.0
Q ss_pred eeEecccccccccccccCcC
Q 043865 134 VMYCRCKTSFCYECGGNLKS 153 (203)
Q Consensus 134 hm~C~C~~~FC~~C~~~~~~ 153 (203)
-++=.||+.||..|...|..
T Consensus 11 Pv~l~CGH~FC~~Cl~~~~~ 30 (42)
T PF15227_consen 11 PVSLPCGHSFCRSCLERLWK 30 (42)
T ss_dssp EEE-SSSSEEEHHHHHHHHC
T ss_pred ccccCCcCHHHHHHHHHHHH
Confidence 46667999999999888775
No 66
>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=71.81 E-value=3.5 Score=22.07 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=12.9
Q ss_pred CCCCCCCceeEec--CCcceeEe-ccc
Q 043865 117 ARRPACGSCVERK--EGCRVMYC-RCK 140 (203)
Q Consensus 117 k~CP~C~~~iek~--~GCnhm~C-~C~ 140 (203)
++||+|+..+++. +|=+...| +|.
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCc
Confidence 5799999988765 45555556 554
No 67
>PHA02926 zinc finger-like protein; Provisional
Probab=71.32 E-value=1 Score=36.35 Aligned_cols=37 Identities=27% Similarity=0.666 Sum_probs=26.5
Q ss_pred CCccccccccCCcCCCCCCccccccccccchhHHHHHHHHhccCCCCCCCCceeEe
Q 043865 73 PNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVER 128 (203)
Q Consensus 73 ~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek 128 (203)
+.|++.||+.|-..|..... + ....+.||-|+.....
T Consensus 195 ~~CnHsFCl~CIr~Wr~~r~--~-----------------~~~~rsCPiCR~~f~~ 231 (242)
T PHA02926 195 DSCNHIFCITCINIWHRTRR--E-----------------TGASDNCPICRTRFRN 231 (242)
T ss_pred CCCCchHHHHHHHHHHHhcc--c-----------------cCcCCcCCCCcceeee
Confidence 36999999999998875321 0 1345789999987653
No 68
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=71.32 E-value=0.76 Score=38.82 Aligned_cols=30 Identities=13% Similarity=0.204 Sum_probs=22.3
Q ss_pred cCCCCCCCCceeEec-CCcceeEe-ccccccc
Q 043865 115 HGARRPACGSCVERK-EGCRVMYC-RCKTSFC 144 (203)
Q Consensus 115 ~~k~CP~C~~~iek~-~GCnhm~C-~C~~~FC 144 (203)
-|.+||+|+..+.+. -.=|...| .|+|+|=
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 478899998888765 34567788 6888763
No 69
>PF14149 YhfH: YhfH-like protein
Probab=71.27 E-value=0.34 Score=27.72 Aligned_cols=31 Identities=23% Similarity=0.608 Sum_probs=23.7
Q ss_pred HHHHhccCCCCCCCCceeEecCCcceeEe-cc
Q 043865 109 KLVERMHGARRPACGSCVERKEGCRVMYC-RC 139 (203)
Q Consensus 109 ~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~C 139 (203)
++.++...|.|+.||..|+-..-|..++| +|
T Consensus 6 eFfrnLp~K~C~~CG~~i~EQ~E~Y~n~C~~C 37 (37)
T PF14149_consen 6 EFFRNLPPKKCTECGKEIEEQAECYGNECDRC 37 (37)
T ss_pred HHHHhCCCcccHHHHHHHHHHHHHHhCcCCCC
Confidence 34456677999999999988777777777 55
No 70
>PF06796 NapE: Periplasmic nitrate reductase protein NapE; InterPro: IPR010649 This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides. NapE is thought to be a transmembrane protein [].
Probab=70.92 E-value=17 Score=22.85 Aligned_cols=31 Identities=19% Similarity=0.146 Sum_probs=20.4
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043865 167 CHHYCAIISGLILIFTVLGVLGGVIYGIYCV 197 (203)
Q Consensus 167 ~~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~ 197 (203)
-.+..+.+.+..++|.+|++..+-.||+.+-
T Consensus 15 ~~E~~~flfl~~~l~PiL~v~~Vg~YGF~VW 45 (56)
T PF06796_consen 15 RSELKAFLFLAVVLFPILAVAFVGGYGFIVW 45 (56)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555556677788887777777776543
No 71
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=70.86 E-value=3.9 Score=25.24 Aligned_cols=35 Identities=31% Similarity=0.508 Sum_probs=19.4
Q ss_pred CceeCCCCCCCceeeecCc-----cccCCCCceeCCCcccc
Q 043865 43 ERSYCPNRNCMALVVNEGE-----INYGTLKKARCPNCKQW 78 (203)
Q Consensus 43 ~~~~Cp~~~C~~~~~~~~~-----~~~~~~~~~~C~~C~~~ 78 (203)
+.+.||||+|-.- ..++. +.+......+|..|.+.
T Consensus 5 gvl~C~Np~CITn-~~E~v~~~F~v~~~~~~~~rC~YCe~~ 44 (52)
T PF02748_consen 5 GVLKCPNPNCITN-SNEPVESRFYVIDKEPIKLRCHYCERI 44 (52)
T ss_dssp SSSE-SSTTBTTT--TSSS--EEEEEETTTCEEEETTT--E
T ss_pred eEEEcCCCCcccC-CCCCCCceEEEEeCCCCEEEeeCCCCE
Confidence 5688999999654 11111 11234678899888765
No 72
>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=70.58 E-value=0.84 Score=38.42 Aligned_cols=30 Identities=20% Similarity=0.442 Sum_probs=23.6
Q ss_pred ccCCCCCCCCceeEec-CCcceeEe-cccccc
Q 043865 114 MHGARRPACGSCVERK-EGCRVMYC-RCKTSF 143 (203)
Q Consensus 114 ~~~k~CP~C~~~iek~-~GCnhm~C-~C~~~F 143 (203)
..|.+||+|+..+.+. -.=|.+.| .|++||
T Consensus 24 ~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 24 GVWTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CCeeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 3589999999988876 34566889 799986
No 73
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=70.21 E-value=4.4 Score=29.22 Aligned_cols=30 Identities=23% Similarity=0.546 Sum_probs=22.2
Q ss_pred ceeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 44 RSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 44 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
..+|| +|++.+++... +......|++|++.
T Consensus 2 m~FCp--~Cgsll~p~~~---~~~~~l~C~kCgye 31 (113)
T COG1594 2 MRFCP--KCGSLLYPKKD---DEGGKLVCRKCGYE 31 (113)
T ss_pred ccccC--CccCeeEEeEc---CCCcEEECCCCCcc
Confidence 46788 69999988654 22448889888876
No 74
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=68.50 E-value=0.98 Score=26.43 Aligned_cols=33 Identities=24% Similarity=0.369 Sum_probs=21.8
Q ss_pred CCCCCceeEecCCcceeEecccccccccccccCcC
Q 043865 119 RPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKS 153 (203)
Q Consensus 119 CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~ 153 (203)
||-|...++. +=.-+.-.|++.|++.|...|-.
T Consensus 3 C~IC~~~~~~--~~~~~~l~C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 3 CPICLEEFED--GEKVVKLPCGHVFHRSCIKEWLK 35 (44)
T ss_dssp ETTTTCBHHT--TSCEEEETTSEEEEHHHHHHHHH
T ss_pred CcCCChhhcC--CCeEEEccCCCeeCHHHHHHHHH
Confidence 5555555543 22233447999999999998875
No 75
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=68.37 E-value=7.2 Score=29.45 Aligned_cols=19 Identities=37% Similarity=0.634 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHhhhhhhcc
Q 043865 184 LGVLGGVIYGIYCVIKRVL 202 (203)
Q Consensus 184 l~~~~~~~~~~~~~~~~~~ 202 (203)
+++|+.+..+||.++|+|+
T Consensus 126 ~g~ll~i~~giy~~~r~~~ 144 (145)
T PF10661_consen 126 GGILLAICGGIYVVLRKVW 144 (145)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 3344445778899999875
No 76
>PF12773 DZR: Double zinc ribbon
Probab=68.28 E-value=2.4 Score=25.51 Aligned_cols=12 Identities=25% Similarity=0.409 Sum_probs=6.6
Q ss_pred CCCCCCCCceeE
Q 043865 116 GARRPACGSCVE 127 (203)
Q Consensus 116 ~k~CP~C~~~ie 127 (203)
.+.||+|+..+.
T Consensus 29 ~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 29 KKICPNCGAENP 40 (50)
T ss_pred CCCCcCCcCCCc
Confidence 345666665544
No 77
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.23 E-value=9.5 Score=25.03 Aligned_cols=23 Identities=30% Similarity=0.621 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhh
Q 043865 178 ILIFTVLGVLGGVIYGIYCVIKR 200 (203)
Q Consensus 178 ~~~f~~l~~~~~~~~~~~~~~~~ 200 (203)
.+++++|++|++++-|+|+.-|.
T Consensus 6 ail~ivl~ll~G~~~G~fiark~ 28 (71)
T COG3763 6 AILLIVLALLAGLIGGFFIARKQ 28 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34677788888888887776554
No 78
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=66.93 E-value=3.4 Score=40.69 Aligned_cols=20 Identities=20% Similarity=0.360 Sum_probs=16.5
Q ss_pred CCCCceeCCCccccccccCC
Q 043865 65 GTLKKARCPNCKQWFCFQCK 84 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~C~~C~ 84 (203)
++...+-|..|+.-.|.-|-
T Consensus 32 ~Ge~FVAC~eC~FPVCrpCY 51 (1079)
T PLN02638 32 DGEPFVACDVCAFPVCRPCY 51 (1079)
T ss_pred CCCEEEEeccCCCccccchh
Confidence 45788999999999997665
No 79
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=66.44 E-value=0.93 Score=25.96 Aligned_cols=16 Identities=31% Similarity=0.731 Sum_probs=13.2
Q ss_pred cccccccccccccCcC
Q 043865 138 RCKTSFCYECGGNLKS 153 (203)
Q Consensus 138 ~C~~~FC~~C~~~~~~ 153 (203)
.|||.||..|...|..
T Consensus 16 ~C~H~fC~~C~~~~~~ 31 (41)
T PF00097_consen 16 PCGHSFCRDCLRKWLE 31 (41)
T ss_dssp TTSEEEEHHHHHHHHH
T ss_pred cCCCcchHHHHHHHHH
Confidence 6899999999887765
No 80
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.28 E-value=2.4 Score=34.36 Aligned_cols=21 Identities=24% Similarity=0.759 Sum_probs=17.2
Q ss_pred CCCCceeCCCccccccccCCcCC
Q 043865 65 GTLKKARCPNCKQWFCFQCKVAW 87 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~C~~C~~~~ 87 (203)
...+.+++ ||+.||+-|.-.|
T Consensus 57 akdPVvTl--CGHLFCWpClyqW 77 (230)
T KOG0823|consen 57 AKDPVVTL--CGHLFCWPCLYQW 77 (230)
T ss_pred cCCCEEee--cccceehHHHHHH
Confidence 34666777 9999999999888
No 81
>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=65.02 E-value=17 Score=21.42 Aligned_cols=26 Identities=27% Similarity=0.466 Sum_probs=15.6
Q ss_pred CCCCCCCce-eEecCCcceeEe-ccccc
Q 043865 117 ARRPACGSC-VERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 117 k~CP~C~~~-iek~~GCnhm~C-~C~~~ 142 (203)
-.||+|+.. +-+..+=....| .|+++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 459999984 333344455666 46653
No 82
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=64.95 E-value=7.3 Score=36.97 Aligned_cols=50 Identities=12% Similarity=0.195 Sum_probs=29.9
Q ss_pred hhcCCHHHHHHHHHHHHHhhcc-CC-----CceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 19 KLMIPSNLFSKWCDVLCEDYVL-GF-----ERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 19 ~~~l~~e~~~~y~~~~~~~~i~-~~-----~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
..-|+.++.++|+++.++.+.. .+ ..+-|. -|+..+.+.+ .+|+.|...|
T Consensus 1086 ~e~l~~a~kq~ye~La~~iFsk~~p~d~~~~~vdc~--~cg~~i~~~~---------~~c~ec~~kf 1141 (1189)
T KOG2041|consen 1086 FEELDDAEKQEYENLAFRIFSKNPPVDPNSAKVDCS--VCGAKIDPYD---------LQCSECQTKF 1141 (1189)
T ss_pred hhhCCHHHHHHHHHHHHHHhccCCCCCCCccceeee--ecCCcCCccC---------CCChhhcCcC
Confidence 3447778899999998887654 21 224443 2554443322 4677776654
No 83
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=64.85 E-value=6.3 Score=39.51 Aligned_cols=18 Identities=33% Similarity=0.887 Sum_probs=10.9
Q ss_pred ceeCCCcccc----ccccCCcC
Q 043865 69 KARCPNCKQW----FCFQCKVA 86 (203)
Q Consensus 69 ~~~C~~C~~~----~C~~C~~~ 86 (203)
...||.|+.. +|..|+..
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~ 688 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTH 688 (1337)
T ss_pred EEECCCCCCccccccCcccCCc
Confidence 3677777753 56666543
No 84
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=64.79 E-value=7.1 Score=25.17 Aligned_cols=28 Identities=21% Similarity=0.408 Sum_probs=19.6
Q ss_pred cCCCCCCCCceeEec---CCcceeEe-ccccc
Q 043865 115 HGARRPACGSCVERK---EGCRVMYC-RCKTS 142 (203)
Q Consensus 115 ~~k~CP~C~~~iek~---~GCnhm~C-~C~~~ 142 (203)
..|+||.|+..+.+. +|=-...| .|+..
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 569999999866554 55555667 57764
No 85
>PLN02189 cellulose synthase
Probab=64.60 E-value=4.6 Score=39.64 Aligned_cols=20 Identities=20% Similarity=0.351 Sum_probs=16.2
Q ss_pred CCCCceeCCCccccccccCC
Q 043865 65 GTLKKARCPNCKQWFCFQCK 84 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~C~~C~ 84 (203)
++...+.|+.|+.-.|..|-
T Consensus 49 ~g~~fvaC~~C~fpvCr~Cy 68 (1040)
T PLN02189 49 DGDLFVACNECGFPVCRPCY 68 (1040)
T ss_pred CCCEEEeeccCCCccccchh
Confidence 35678999999999997665
No 86
>PLN03086 PRLI-interacting factor K; Provisional
Probab=64.17 E-value=4.1 Score=37.52 Aligned_cols=29 Identities=28% Similarity=0.673 Sum_probs=24.4
Q ss_pred cCCCCCC--CCceeEecCCcceeEe-cccccc
Q 043865 115 HGARRPA--CGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 115 ~~k~CP~--C~~~iek~~GCnhm~C-~C~~~F 143 (203)
+...||+ |+..+.+.+.=+|..| .|+..|
T Consensus 432 ~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 432 HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred cceeCCcccccceeeccccccCccCCCCCCcc
Confidence 4467995 9999999999999999 798765
No 87
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=64.01 E-value=6.1 Score=27.86 Aligned_cols=29 Identities=21% Similarity=0.445 Sum_probs=19.8
Q ss_pred cCCCCCCCCcee---EecCCcceeEe-cccccc
Q 043865 115 HGARRPACGSCV---ERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 115 ~~k~CP~C~~~i---ek~~GCnhm~C-~C~~~F 143 (203)
..-.||+|+... .+..|=-|..| .||+.+
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 456799999432 23346668999 798874
No 88
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=63.97 E-value=8.1 Score=24.49 Aligned_cols=25 Identities=20% Similarity=0.566 Sum_probs=19.5
Q ss_pred CCCCCCc----eeEecCCcceeEe-ccccc
Q 043865 118 RRPACGS----CVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 118 ~CP~C~~----~iek~~GCnhm~C-~C~~~ 142 (203)
.||+|+. ...+..|=.++.| .|||.
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 5999986 3556677789999 79985
No 89
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=63.65 E-value=2.3 Score=24.02 Aligned_cols=30 Identities=20% Similarity=0.387 Sum_probs=20.1
Q ss_pred CCCCCceeEecCCcceeEe-cccccccccccccCcC
Q 043865 119 RPACGSCVERKEGCRVMYC-RCKTSFCYECGGNLKS 153 (203)
Q Consensus 119 CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~ 153 (203)
||-|...+ -+-+.- .|++.||+.|...|..
T Consensus 2 C~iC~~~~-----~~~~~~~~C~H~~c~~C~~~~~~ 32 (45)
T cd00162 2 CPICLEEF-----REPVVLLPCGHVFCRSCIDKWLK 32 (45)
T ss_pred CCcCchhh-----hCceEecCCCChhcHHHHHHHHH
Confidence 56665554 123334 4999999999988765
No 90
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=63.47 E-value=2.6 Score=25.87 Aligned_cols=24 Identities=29% Similarity=0.592 Sum_probs=12.1
Q ss_pred CCCCCCceeEecCCcc--eeEe-cccc
Q 043865 118 RRPACGSCVERKEGCR--VMYC-RCKT 141 (203)
Q Consensus 118 ~CP~C~~~iek~~GCn--hm~C-~C~~ 141 (203)
+|++|+...-+.++=. .+.| +|++
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCc
Confidence 4566665555543322 4555 5554
No 91
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=63.28 E-value=7.7 Score=25.58 Aligned_cols=25 Identities=24% Similarity=0.594 Sum_probs=19.6
Q ss_pred CCCCCCc----eeEecCCcceeEe-ccccc
Q 043865 118 RRPACGS----CVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 118 ~CP~C~~----~iek~~GCnhm~C-~C~~~ 142 (203)
.||+|+. ...+..|=.++.| .|||.
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 5999986 4556688888999 79986
No 92
>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=62.71 E-value=4.3 Score=26.08 Aligned_cols=38 Identities=18% Similarity=0.348 Sum_probs=20.7
Q ss_pred hccCCCCCCCCceeEecCCcceeEe-cccccccccccccCc
Q 043865 113 RMHGARRPACGSCVERKEGCRVMYC-RCKTSFCYECGGNLK 152 (203)
Q Consensus 113 ~~~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~ 152 (203)
+.....|+.|+.... --=..-.| .||.-||-.|.....
T Consensus 6 d~~~~~C~~C~~~F~--~~~rrhhCr~CG~~vC~~Cs~~~~ 44 (69)
T PF01363_consen 6 DSEASNCMICGKKFS--LFRRRHHCRNCGRVVCSSCSSQRI 44 (69)
T ss_dssp GGG-SB-TTT--B-B--SSS-EEE-TTT--EEECCCS-EEE
T ss_pred CCCCCcCcCcCCcCC--CceeeEccCCCCCEECCchhCCEE
Confidence 455678999999883 33566789 699999999976544
No 93
>COG3630 OadG Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, gamma subunit [Energy production and conversion]
Probab=62.65 E-value=17 Score=24.68 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 043865 174 ISGLILIFTVLGVLGGVIYGIYCVIKR 200 (203)
Q Consensus 174 ~~~~~~~f~~l~~~~~~~~~~~~~~~~ 200 (203)
+.+.-+-|++|++|.++++++==++.+
T Consensus 15 vlGmg~VflfL~iLi~~~~~m~~~v~r 41 (84)
T COG3630 15 VLGMGFVFLFLSILIYAMRGMGAVVRR 41 (84)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445556688888886666665444433
No 94
>PRK00420 hypothetical protein; Validated
Probab=62.64 E-value=5.7 Score=28.66 Aligned_cols=30 Identities=20% Similarity=0.275 Sum_probs=22.4
Q ss_pred cCCCCCCCCceeEe-cCCcceeEecccccccccccccCcC
Q 043865 115 HGARRPACGSCVER-KEGCRVMYCRCKTSFCYECGGNLKS 153 (203)
Q Consensus 115 ~~k~CP~C~~~iek-~~GCnhm~C~C~~~FC~~C~~~~~~ 153 (203)
....||.|+.+..+ .+ |..||-.||....-
T Consensus 22 l~~~CP~Cg~pLf~lk~---------g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 22 LSKHCPVCGLPLFELKD---------GEVVCPVHGKVYIV 52 (112)
T ss_pred ccCCCCCCCCcceecCC---------CceECCCCCCeeee
Confidence 44799999999987 34 45677788776653
No 95
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=62.51 E-value=2.7 Score=35.10 Aligned_cols=33 Identities=21% Similarity=0.446 Sum_probs=26.6
Q ss_pred hccCCCCCCCCceeEec-CCcceeEe-cccccccc
Q 043865 113 RMHGARRPACGSCVERK-EGCRVMYC-RCKTSFCY 145 (203)
Q Consensus 113 ~~~~k~CP~C~~~iek~-~GCnhm~C-~C~~~FC~ 145 (203)
+..|..||.|+..+-+. -+=|...| +|+|+|=-
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri 59 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRI 59 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCccccc
Confidence 45789999999988775 56788889 79998743
No 96
>TIGR02973 nitrate_rd_NapE periplasmic nitrate reductase, NapE protein. NapE, homologous to TorE (TIGR02972), is a membrane protein of unknown function that is part of the periplasmic nitrate reductase system; it may be part of the enzyme complex. The periplasmic nitrate reductase allows for nitrate respiration in anaerobic conditions.
Probab=62.34 E-value=28 Score=20.46 Aligned_cols=28 Identities=21% Similarity=0.220 Sum_probs=17.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043865 169 HYCAIISGLILIFTVLGVLGGVIYGIYC 196 (203)
Q Consensus 169 ~~~~~~~~~~~~f~~l~~~~~~~~~~~~ 196 (203)
+..+...+..++|.+|++..+-.|++..
T Consensus 4 El~~flfl~~~l~PiLsV~~V~~YGF~v 31 (42)
T TIGR02973 4 ELNTFLFLAAVIWPVLSVITVGGYGFAV 31 (42)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455566777777777776777654
No 97
>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins.
Probab=61.93 E-value=4.6 Score=28.45 Aligned_cols=18 Identities=33% Similarity=0.781 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhh
Q 043865 178 ILIFTVLGVLGGVIYGIYCVI 198 (203)
Q Consensus 178 ~~~f~~l~~~~~~~~~~~~~~ 198 (203)
++.|+.+.+| +|.||.++
T Consensus 68 lls~v~IlVi---ly~IyYFV 85 (101)
T PF06024_consen 68 LLSFVCILVI---LYAIYYFV 85 (101)
T ss_pred HHHHHHHHHH---HhhheEEE
Confidence 3334444444 45555444
No 98
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=61.38 E-value=6.7 Score=36.85 Aligned_cols=14 Identities=29% Similarity=0.589 Sum_probs=8.4
Q ss_pred ccCCCCCCCCceeE
Q 043865 114 MHGARRPACGSCVE 127 (203)
Q Consensus 114 ~~~k~CP~C~~~ie 127 (203)
.+.+.||+||....
T Consensus 39 ~~~~fC~~CG~~~~ 52 (645)
T PRK14559 39 VDEAHCPNCGAETG 52 (645)
T ss_pred cccccccccCCccc
Confidence 34466777776553
No 99
>PLN02400 cellulose synthase
Probab=61.00 E-value=6.5 Score=38.83 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=16.7
Q ss_pred CCCCceeCCCccccccccCC
Q 043865 65 GTLKKARCPNCKQWFCFQCK 84 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~C~~C~ 84 (203)
++...+-|..|+.-.|.-|-
T Consensus 51 dGe~FVAC~eCaFPVCRpCY 70 (1085)
T PLN02400 51 TGDVFVACNECAFPVCRPCY 70 (1085)
T ss_pred CCCEEEEEccCCCccccchh
Confidence 45788999999999997665
No 100
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=60.73 E-value=9.3 Score=30.75 Aligned_cols=21 Identities=24% Similarity=0.490 Sum_probs=15.1
Q ss_pred CCCceeCCCCCCCceeeecCc
Q 043865 41 GFERSYCPNRNCMALVVNEGE 61 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~~~~~~~ 61 (203)
+.+++-||.|+|+.++..+..
T Consensus 135 sSqRIACPRpnCkRiInL~p~ 155 (275)
T KOG4684|consen 135 SSQRIACPRPNCKRIINLDPL 155 (275)
T ss_pred ccceeccCCCCcceeeecCCC
Confidence 456788888889888765443
No 101
>PRK02935 hypothetical protein; Provisional
Probab=60.58 E-value=6.4 Score=27.96 Aligned_cols=24 Identities=21% Similarity=0.649 Sum_probs=16.0
Q ss_pred CCCCceeCCCccccc--------cccCCcCCC
Q 043865 65 GTLKKARCPNCKQWF--------CFQCKVAWH 88 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~--------C~~C~~~~H 88 (203)
.+..++.||+|++.+ |..|++|-+
T Consensus 66 tkavqV~CP~C~K~TKmLGrvD~CM~C~~PLT 97 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLGRVDACMHCNQPLT 97 (110)
T ss_pred ccceeeECCCCCchhhhccceeecCcCCCcCC
Confidence 345667777776544 888887654
No 102
>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=60.53 E-value=6 Score=28.46 Aligned_cols=25 Identities=28% Similarity=0.709 Sum_probs=18.1
Q ss_pred CCCCceeCCCccccc--------cccCCcCCCC
Q 043865 65 GTLKKARCPNCKQWF--------CFQCKVAWHA 89 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~--------C~~C~~~~H~ 89 (203)
.....++||+|++.+ |..|++|-+-
T Consensus 65 tkav~V~CP~C~K~TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 65 TKAVQVECPNCGKQTKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred ccceeeECCCCCChHhhhchhhccCcCCCcCcc
Confidence 346778888888766 8888876543
No 103
>PRK14750 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=60.48 E-value=23 Score=18.92 Aligned_cols=10 Identities=30% Similarity=0.667 Sum_probs=4.6
Q ss_pred HHHHHHHHHH
Q 043865 185 GVLGGVIYGI 194 (203)
Q Consensus 185 ~~~~~~~~~~ 194 (203)
.++|+++|.+
T Consensus 14 lLl~YLvYAL 23 (29)
T PRK14750 14 LLLGYLVYAL 23 (29)
T ss_pred HHHHHHHHHH
Confidence 3344445544
No 104
>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=60.13 E-value=7.8 Score=23.75 Aligned_cols=11 Identities=27% Similarity=0.486 Sum_probs=9.2
Q ss_pred CCCCCCCceeE
Q 043865 117 ARRPACGSCVE 127 (203)
Q Consensus 117 k~CP~C~~~ie 127 (203)
|+||.|+-.-+
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 78999998666
No 105
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=59.78 E-value=9.4 Score=22.42 Aligned_cols=14 Identities=21% Similarity=0.534 Sum_probs=5.9
Q ss_pred HHHHhccCCCCCCC
Q 043865 109 KLVERMHGARRPAC 122 (203)
Q Consensus 109 ~~~~~~~~k~CP~C 122 (203)
.+.+......||+|
T Consensus 30 ~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 30 KYFRHRSNPKCPNC 43 (43)
T ss_dssp HHTTT-SS-B-TTT
T ss_pred HHHhcCCCCCCcCC
Confidence 34333333479987
No 106
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=59.61 E-value=6.6 Score=24.89 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=18.7
Q ss_pred eCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 46 YCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 46 ~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
.|- .|+..+...+. ...+.||.|+...
T Consensus 9 ~Ct--SCg~~i~~~~~-----~~~F~CPnCG~~~ 35 (59)
T PRK14890 9 KCT--SCGIEIAPREK-----AVKFLCPNCGEVI 35 (59)
T ss_pred ccc--CCCCcccCCCc-----cCEeeCCCCCCee
Confidence 454 47776655443 6789999998874
No 107
>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=59.53 E-value=11 Score=22.01 Aligned_cols=8 Identities=50% Similarity=1.053 Sum_probs=4.5
Q ss_pred CCCCCCce
Q 043865 118 RRPACGSC 125 (203)
Q Consensus 118 ~CP~C~~~ 125 (203)
.||.|+..
T Consensus 2 ~Cp~Cg~~ 9 (43)
T PF08271_consen 2 KCPNCGSK 9 (43)
T ss_dssp SBTTTSSS
T ss_pred CCcCCcCC
Confidence 36666653
No 108
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=59.22 E-value=7.8 Score=26.58 Aligned_cols=28 Identities=21% Similarity=0.580 Sum_probs=22.8
Q ss_pred CCCCCCCCceeEecCCcceeEe-cccccc
Q 043865 116 GARRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
--.||.|+....|..+=---.| .||+.|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence 4589999999988888777788 677766
No 109
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=59.04 E-value=11 Score=23.08 Aligned_cols=22 Identities=27% Similarity=0.236 Sum_probs=13.5
Q ss_pred chhhHHHHHHHHHHHHHHHHHH
Q 043865 167 CHHYCAIISGLILIFTVLGVLG 188 (203)
Q Consensus 167 ~~~~~~~~~~~~~~f~~l~~~~ 188 (203)
.+++.+++++.+++++++.++.
T Consensus 13 ~~nk~a~~gl~il~~~vl~ai~ 34 (56)
T PF12911_consen 13 RRNKLAVIGLIILLILVLLAIF 34 (56)
T ss_pred HhCchHHHHHHHHHHHHHHHHH
Confidence 3567788877766655554443
No 110
>PLN02436 cellulose synthase A
Probab=58.67 E-value=6.9 Score=38.64 Aligned_cols=47 Identities=21% Similarity=0.361 Sum_probs=30.5
Q ss_pred CCCCceeCCCccccccccCCcCCCCCCccccccccccchhHHHHHHHHhccCCCCCCCCceeEecCCccee
Q 043865 65 GTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVM 135 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm 135 (203)
++...+-|..|+.-.|..|- ||.. +++.+.||+|+....+-.|+..+
T Consensus 51 dGe~FVACn~C~fpvCr~Cy----------eyer--------------~eg~~~Cpqckt~Y~r~kgs~~~ 97 (1094)
T PLN02436 51 DGEPFVACNECAFPVCRPCY----------EYER--------------REGNQACPQCKTRYKRIKGSPRV 97 (1094)
T ss_pred CCCEEEeeccCCCccccchh----------hhhh--------------hcCCccCcccCCchhhccCCCCc
Confidence 45788999999999997554 3321 34556677777766655444433
No 111
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=58.36 E-value=9.4 Score=27.51 Aligned_cols=27 Identities=26% Similarity=0.486 Sum_probs=19.6
Q ss_pred CCCCCCCceeEec--CCcceeEe-cccccc
Q 043865 117 ARRPACGSCVERK--EGCRVMYC-RCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~--~GCnhm~C-~C~~~F 143 (203)
+.||+|+.++.-. ++=+.+.| .|||++
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~ 32 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEE 32 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcch
Confidence 6799999887752 23338889 698875
No 112
>PHA02929 N1R/p28-like protein; Provisional
Probab=58.15 E-value=3.4 Score=33.85 Aligned_cols=16 Identities=38% Similarity=1.182 Sum_probs=12.3
Q ss_pred CCccccccccCCcCCC
Q 043865 73 PNCKQWFCFQCKVAWH 88 (203)
Q Consensus 73 ~~C~~~~C~~C~~~~H 88 (203)
+.|++.||..|-..|.
T Consensus 198 ~~C~H~FC~~CI~~Wl 213 (238)
T PHA02929 198 SNCNHVFCIECIDIWK 213 (238)
T ss_pred CCCCCcccHHHHHHHH
Confidence 4688888888887765
No 113
>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=57.48 E-value=6.2 Score=23.11 Aligned_cols=28 Identities=18% Similarity=0.567 Sum_probs=16.6
Q ss_pred CceeCCCccccccccCCcCCCCCCcccccc
Q 043865 68 KKARCPNCKQWFCFQCKVAWHAGYRCEESG 97 (203)
Q Consensus 68 ~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~ 97 (203)
..+.|+.|+..||.+-+.+- ...|....
T Consensus 12 ~~~~C~~C~~~FC~~Hr~~e--~H~C~~~~ 39 (43)
T PF01428_consen 12 LPFKCKHCGKSFCLKHRLPE--DHNCSKLQ 39 (43)
T ss_dssp SHEE-TTTS-EE-TTTHSTT--TCT-SSTT
T ss_pred CCeECCCCCcccCccccCcc--ccCCcchh
Confidence 45899999999999887652 23566543
No 114
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=57.39 E-value=9.5 Score=28.25 Aligned_cols=25 Identities=40% Similarity=0.878 Sum_probs=19.2
Q ss_pred cCCCCCCCCceeEecCCcceeEeccccccccccc
Q 043865 115 HGARRPACGSCVERKEGCRVMYCRCKTSFCYECG 148 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~ 148 (203)
....||.|+.+..+.+| .-||-+|+
T Consensus 27 L~~hCp~Cg~PLF~KdG---------~v~CPvC~ 51 (131)
T COG1645 27 LAKHCPKCGTPLFRKDG---------EVFCPVCG 51 (131)
T ss_pred HHhhCcccCCcceeeCC---------eEECCCCC
Confidence 35789999999988664 56666666
No 115
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=57.25 E-value=6.7 Score=25.38 Aligned_cols=22 Identities=23% Similarity=0.603 Sum_probs=9.2
Q ss_pred CCCCCCCCceeEec---CCcceeEe
Q 043865 116 GARRPACGSCVERK---EGCRVMYC 137 (203)
Q Consensus 116 ~k~CP~C~~~iek~---~GCnhm~C 137 (203)
.-+|++|....... +||.|+.|
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fC 31 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFC 31 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-
T ss_pred hcCCcHHHHHhcCCceeccCccHHH
Confidence 35899999886543 66766655
No 116
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=57.04 E-value=13 Score=30.59 Aligned_cols=39 Identities=21% Similarity=0.445 Sum_probs=24.2
Q ss_pred CCCceeCCCCCCCceeeecCc----cc-----cCCCCceeCCCccccc
Q 043865 41 GFERSYCPNRNCMALVVNEGE----IN-----YGTLKKARCPNCKQWF 79 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~~~~~~~----~~-----~~~~~~~~C~~C~~~~ 79 (203)
...++.||.|+|+.++...+. .. ......+.|..|+..|
T Consensus 120 sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~F 167 (256)
T PF09788_consen 120 SSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTF 167 (256)
T ss_pred ccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcE
Confidence 456788999999998864433 10 1234556676655544
No 117
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=55.98 E-value=11 Score=22.34 Aligned_cols=11 Identities=27% Similarity=0.486 Sum_probs=6.5
Q ss_pred CCCCCCCceeE
Q 043865 117 ARRPACGSCVE 127 (203)
Q Consensus 117 k~CP~C~~~ie 127 (203)
-+||.|+..|.
T Consensus 20 irC~~CG~rIl 30 (44)
T smart00659 20 VRCRECGYRIL 30 (44)
T ss_pred eECCCCCceEE
Confidence 45666666553
No 118
>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=55.92 E-value=8.3 Score=26.06 Aligned_cols=29 Identities=31% Similarity=0.675 Sum_probs=16.0
Q ss_pred cCCCCCCCC----c--eeEecCCcceeEe-cccccc
Q 043865 115 HGARRPACG----S--CVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 115 ~~k~CP~C~----~--~iek~~GCnhm~C-~C~~~F 143 (203)
..-.||.|+ + -+.+..|=-+++| .||..|
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 446899999 2 3455678888999 698766
No 119
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=55.65 E-value=11 Score=26.47 Aligned_cols=29 Identities=21% Similarity=0.654 Sum_probs=20.0
Q ss_pred eeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
.+|| .|++.++.+.. +....+.|+.|.+.
T Consensus 2 ~FCP--~Cgn~Live~g---~~~~rf~C~tCpY~ 30 (105)
T KOG2906|consen 2 LFCP--TCGNMLIVESG---ESCNRFSCRTCPYV 30 (105)
T ss_pred cccC--CCCCEEEEecC---CeEeeEEcCCCCce
Confidence 4688 59999988776 23566667666554
No 120
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=55.43 E-value=2.4 Score=35.43 Aligned_cols=20 Identities=25% Similarity=0.951 Sum_probs=15.8
Q ss_pred eeCCCccccccccCCcCCCC
Q 043865 70 ARCPNCKQWFCFQCKVAWHA 89 (203)
Q Consensus 70 ~~C~~C~~~~C~~C~~~~H~ 89 (203)
-.|.-||+.||+.|-..|-.
T Consensus 252 pSaTpCGHiFCWsCI~~w~~ 271 (293)
T KOG0317|consen 252 PSATPCGHIFCWSCILEWCS 271 (293)
T ss_pred CCcCcCcchHHHHHHHHHHc
Confidence 35667999999999987753
No 121
>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=55.22 E-value=9.2 Score=27.31 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=19.1
Q ss_pred CCCCCCCceeEecCCcceeEe-cccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
-.||+|+.-..=.+|=+ +.| -|+++|
T Consensus 3 p~CP~C~seytY~dg~~-~iCpeC~~EW 29 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQ-LICPSCLYEW 29 (109)
T ss_pred CcCCcCCCcceEecCCe-eECccccccc
Confidence 47999999887777754 667 476665
No 122
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=55.04 E-value=8.5 Score=22.19 Aligned_cols=13 Identities=31% Similarity=0.700 Sum_probs=9.1
Q ss_pred CCCCCCceeEecC
Q 043865 118 RRPACGSCVERKE 130 (203)
Q Consensus 118 ~CP~C~~~iek~~ 130 (203)
+||+|+...+...
T Consensus 1 ~CP~C~~~l~~~~ 13 (41)
T PF13453_consen 1 KCPRCGTELEPVR 13 (41)
T ss_pred CcCCCCcccceEE
Confidence 4888888766553
No 123
>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=54.56 E-value=10 Score=19.51 Aligned_cols=11 Identities=36% Similarity=0.727 Sum_probs=8.4
Q ss_pred CCceeCCCccc
Q 043865 67 LKKARCPNCKQ 77 (203)
Q Consensus 67 ~~~~~C~~C~~ 77 (203)
...+.||.|+.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 56788888874
No 124
>PF11395 DUF2873: Protein of unknown function (DUF2873); InterPro: IPR021532 This entry is represented by the human SARS coronavirus, Orf7b; it is a family of uncharacterised viral proteins.
Probab=54.29 E-value=28 Score=19.85 Aligned_cols=17 Identities=24% Similarity=0.172 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHH
Q 043865 176 GLILIFTVLGVLGGVIY 192 (203)
Q Consensus 176 ~~~~~f~~l~~~~~~~~ 192 (203)
+..|+|+++++|..+-|
T Consensus 14 l~~llflv~imliif~f 30 (43)
T PF11395_consen 14 LSFLLFLVIIMLIIFWF 30 (43)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34555655555544433
No 125
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=53.90 E-value=8.9 Score=33.13 Aligned_cols=19 Identities=21% Similarity=0.418 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q 043865 177 LILIFTVLGVLGGVIYGIY 195 (203)
Q Consensus 177 ~~~~f~~l~~~~~~~~~~~ 195 (203)
++.++++|++|++++||+|
T Consensus 192 vl~~~fvl~tlaivLFPLW 210 (372)
T KOG2927|consen 192 VLGVLFVLVTLAIVLFPLW 210 (372)
T ss_pred HHHHHHHHHHHHHHhcccC
Confidence 3444445556666665554
No 126
>PLN00209 ribosomal protein S27; Provisional
Probab=53.82 E-value=20 Score=24.47 Aligned_cols=31 Identities=16% Similarity=0.510 Sum_probs=22.2
Q ss_pred eeCCCCCCCceeeecCccccCCCCceeCCCccccccc
Q 043865 45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCF 81 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 81 (203)
+.|| +|.+.-..=.. ....+.|..|+...+.
T Consensus 37 VkCp--~C~n~q~VFSh----A~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 37 VKCQ--GCFNITTVFSH----SQTVVVCGSCQTVLCQ 67 (86)
T ss_pred EECC--CCCCeeEEEec----CceEEEccccCCEeec
Confidence 7888 79876544333 3678999999988764
No 127
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=53.78 E-value=9.6 Score=23.35 Aligned_cols=15 Identities=47% Similarity=0.844 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHH
Q 043865 177 LILIFTVLGVLGGVI 191 (203)
Q Consensus 177 ~~~~f~~l~~~~~~~ 191 (203)
++.+|+++++||++|
T Consensus 6 iV~i~iv~~lLg~~I 20 (50)
T PF12606_consen 6 IVSIFIVMGLLGLSI 20 (50)
T ss_pred HHHHHHHHHHHHHHH
Confidence 455566666666544
No 128
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=53.52 E-value=16 Score=23.73 Aligned_cols=32 Identities=22% Similarity=0.346 Sum_probs=21.9
Q ss_pred ceeCCCCCCCceeeecCccccCCCCceeCCCccccccc
Q 043865 44 RSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCF 81 (203)
Q Consensus 44 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 81 (203)
.+.|| ||++.-..=.. ....++|..|+...+.
T Consensus 19 ~VkCp--dC~N~q~vFsh----ast~V~C~~CG~~l~~ 50 (67)
T COG2051 19 RVKCP--DCGNEQVVFSH----ASTVVTCLICGTTLAE 50 (67)
T ss_pred EEECC--CCCCEEEEecc----CceEEEecccccEEEe
Confidence 37787 79886544333 2678899999887653
No 129
>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=52.79 E-value=8 Score=28.47 Aligned_cols=26 Identities=19% Similarity=0.097 Sum_probs=17.3
Q ss_pred CCCCCCCceeEecCCcceeEe-cccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
+.||+|+...---.. +-++| .||+.|
T Consensus 10 r~Cp~cg~kFYDLnk-~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNR-RPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCC-CCccCCCcCCcc
Confidence 568888876654333 66777 677664
No 130
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=52.52 E-value=21 Score=24.30 Aligned_cols=31 Identities=19% Similarity=0.532 Sum_probs=22.3
Q ss_pred eeCCCCCCCceeeecCccccCCCCceeCCCccccccc
Q 043865 45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCF 81 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 81 (203)
+.|| +|.+.-..=.. ....+.|..|+...|.
T Consensus 36 VkCp--~C~n~q~VFSh----A~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCP--GCSQITTVFSH----AQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECC--CCCCeeEEEec----CceEEEccccCCEeec
Confidence 7888 79876544332 3678999999988774
No 131
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=52.51 E-value=14 Score=20.47 Aligned_cols=25 Identities=16% Similarity=0.302 Sum_probs=12.8
Q ss_pred CCCCCCCceeEecCCcceeEe-cccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKT 141 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~ 141 (203)
+.|+.|+....-..-=+.+.| .|+.
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCc
Confidence 456667665544333334555 3544
No 132
>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=52.15 E-value=12 Score=34.02 Aligned_cols=33 Identities=21% Similarity=0.558 Sum_probs=26.0
Q ss_pred CCCCCCceeEecCCcceeEe-ccccc-----cccccccc
Q 043865 118 RRPACGSCVERKEGCRVMYC-RCKTS-----FCYECGGN 150 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 150 (203)
+||+|.....--..=|.+.| .||+. .|-.|+..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 69999988776556669999 69976 68888764
No 133
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=51.58 E-value=10 Score=37.47 Aligned_cols=20 Identities=20% Similarity=0.360 Sum_probs=16.7
Q ss_pred CCCCceeCCCccccccccCC
Q 043865 65 GTLKKARCPNCKQWFCFQCK 84 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~C~~C~ 84 (203)
++...+.|..|+.-.|..|-
T Consensus 30 ~Ge~FVAC~eC~fpvCr~cy 49 (1044)
T PLN02915 30 DGQPFVACHVCGFPVCKPCY 49 (1044)
T ss_pred CCCEEEEeccCCCccccchh
Confidence 45788999999999997765
No 134
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=51.53 E-value=3.6 Score=36.52 Aligned_cols=80 Identities=20% Similarity=0.384 Sum_probs=46.6
Q ss_pred CCceeCCCccccccccCCcCCCCCCccccccccccchhHHHHHHHHhccCCCCCCCCceeEecCCcce-eEe-ccccccc
Q 043865 67 LKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRV-MYC-RCKTSFC 144 (203)
Q Consensus 67 ~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GCnh-m~C-~C~~~FC 144 (203)
...+-|..|...+|.-|+..-|++..=-.-.++...++-.+..........+|- --+|=|| |+| .|+-.-|
T Consensus 174 ~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct-------~h~~e~~smyc~~ck~pvc 246 (699)
T KOG4367|consen 174 EATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCT-------DHELENHSMYCVQCKMPVC 246 (699)
T ss_pred hhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhcc-------CCCCCCceEEEEecCChHH
Confidence 456889999999999999988886421000011111110010001111223342 2345555 999 7999999
Q ss_pred ccccccCcC
Q 043865 145 YECGGNLKS 153 (203)
Q Consensus 145 ~~C~~~~~~ 153 (203)
|.|+++.+.
T Consensus 247 ~~clee~kh 255 (699)
T KOG4367|consen 247 YQCLEEGKH 255 (699)
T ss_pred HHHHHhhcc
Confidence 999998774
No 135
>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=50.62 E-value=4 Score=31.06 Aligned_cols=39 Identities=15% Similarity=0.328 Sum_probs=23.7
Q ss_pred ccCCCCCCCCceeEecCCcceeEe----cccccccccccccCc
Q 043865 114 MHGARRPACGSCVERKEGCRVMYC----RCKTSFCYECGGNLK 152 (203)
Q Consensus 114 ~~~k~CP~C~~~iek~~GCnhm~C----~C~~~FC~~C~~~~~ 152 (203)
+.+..||+|+.+|.-..-..-+.= .=--.||+.||++|.
T Consensus 37 ~tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 37 KTITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 456789999999975521111000 014578999988754
No 136
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=50.32 E-value=5.5 Score=21.39 Aligned_cols=16 Identities=25% Similarity=0.661 Sum_probs=13.8
Q ss_pred cccccccccccccCcC
Q 043865 138 RCKTSFCYECGGNLKS 153 (203)
Q Consensus 138 ~C~~~FC~~C~~~~~~ 153 (203)
.|++.||+.|...|..
T Consensus 15 ~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 15 PCGHTFCRSCIRKWLK 30 (39)
T ss_pred cCCChHHHHHHHHHHH
Confidence 6999999999988764
No 137
>PF02468 PsbN: Photosystem II reaction centre N protein (psbN); InterPro: IPR003398 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbN found in PSII. PsbN may have a role in PSII stability, however its actual function unknown. PsbN does not appear to be essential for photoautotrophic growth or normal PSII function.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane
Probab=48.96 E-value=19 Score=21.25 Aligned_cols=19 Identities=26% Similarity=0.338 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q 043865 180 IFTVLGVLGGVIYGIYCVI 198 (203)
Q Consensus 180 ~f~~l~~~~~~~~~~~~~~ 198 (203)
+|+..+++++..|++|-.+
T Consensus 9 i~i~~~lv~~Tgy~iYtaF 27 (43)
T PF02468_consen 9 IFISCLLVSITGYAIYTAF 27 (43)
T ss_pred HHHHHHHHHHHhhhhhhee
Confidence 4445555555568887654
No 138
>PF07243 Phlebovirus_G1: Phlebovirus glycoprotein G1; InterPro: IPR010826 This domain is found in several Phlebovirus glycoprotein G1 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi [].; GO: 0016021 integral to membrane, 0019012 virion
Probab=48.73 E-value=32 Score=31.47 Aligned_cols=56 Identities=21% Similarity=0.415 Sum_probs=33.6
Q ss_pred ccccccccccccCcCCCCCCCCcCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 043865 139 CKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRV 201 (203)
Q Consensus 139 C~~~FC~~C~~~~~~~~~C~~~~~~~~~~~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~~~~~ 201 (203)
|..+=||.|..-|-+ ++|+.--+ ..+-.+++..+++++|.+|+-++|.+=++.+++
T Consensus 399 C~~~~C~fC~~gliN---yQCHTaLS----AlvVStliss~iylil~IL~K~L~~~kliPkkL 454 (526)
T PF07243_consen 399 CEVHHCFFCRHGLIN---YQCHTALS----ALVVSTLISSLIYLILSILSKVLYFFKLIPKKL 454 (526)
T ss_pred hhcceeeehhccccc---ccchhHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 999999999999887 44432111 011112234555666677777777666665554
No 139
>PRK10220 hypothetical protein; Provisional
Probab=48.16 E-value=15 Score=26.33 Aligned_cols=26 Identities=19% Similarity=0.516 Sum_probs=18.5
Q ss_pred CCCCCCCceeEecCCcceeEe-cccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
-.||+|+.-..=.+|=+ +.| -|+++|
T Consensus 4 P~CP~C~seytY~d~~~-~vCpeC~hEW 30 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGM-YICPECAHEW 30 (111)
T ss_pred CcCCCCCCcceEcCCCe-EECCcccCcC
Confidence 47999998887777754 666 466654
No 140
>PHA02929 N1R/p28-like protein; Provisional
Probab=48.07 E-value=8.5 Score=31.56 Aligned_cols=39 Identities=26% Similarity=0.365 Sum_probs=28.1
Q ss_pred cCCCCCCCCceeEecCCcc---eeEecccccccccccccCcC
Q 043865 115 HGARRPACGSCVERKEGCR---VMYCRCKTSFCYECGGNLKS 153 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCn---hm~C~C~~~FC~~C~~~~~~ 153 (203)
....||-|...+...+.-+ -+.-.|+|.||..|..+|..
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~ 214 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK 214 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh
Confidence 3468999999876554222 13346899999999988875
No 141
>PF01405 PsbT: Photosystem II reaction centre T protein; InterPro: IPR001743 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbT found in PSII, which is thought to be associated with the D1 (PsbA) - D2 (PsbD) heterodimer. PsbT may be involved in the formation and/or stabilisation of dimeric PSII complexes, because in the absence of this protein dimeric PSII complexes were found to be less abundant. Furthermore, although PsbT does not confer photo-protection, it is required for the efficient recovery of photo-damaged PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3BZ1_T 1S5L_t 2AXT_t 3KZI_T 3PRQ_T 3BZ2_T 3PRR_T 4FBY_g 3A0H_t 3A0B_T ....
Probab=47.82 E-value=42 Score=18.04 Aligned_cols=17 Identities=29% Similarity=0.782 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHh
Q 043865 179 LIFTVLGVLGGVIYGIY 195 (203)
Q Consensus 179 ~~f~~l~~~~~~~~~~~ 195 (203)
..|++.+.||.+.|.++
T Consensus 6 Y~~ll~~tlgilffAI~ 22 (29)
T PF01405_consen 6 YTFLLIGTLGILFFAIF 22 (29)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhhh
Confidence 34555566666666654
No 142
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=47.81 E-value=37 Score=24.40 Aligned_cols=48 Identities=21% Similarity=0.479 Sum_probs=26.9
Q ss_pred CHHHHHHHHHHHHHhhcc---------CCCceeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 23 PSNLFSKWCDVLCEDYVL---------GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 23 ~~e~~~~y~~~~~~~~i~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
.++.++-.-+.+.+..+. .+-..+|+ +|+..+..... ....||.|+..
T Consensus 40 ~p~~L~f~f~~~~~~t~~egA~L~i~~~p~~~~C~--~Cg~~~~~~~~------~~~~CP~Cgs~ 96 (114)
T PRK03681 40 ETSSLAFCFDLVCRGTVAEGCKLHLEEQEAECWCE--TCQQYVTLLTQ------RVRRCPQCHGD 96 (114)
T ss_pred CHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCeeecCCc------cCCcCcCcCCC
Confidence 355555444444444332 34568888 69876654432 23568887753
No 143
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=47.38 E-value=17 Score=22.65 Aligned_cols=27 Identities=30% Similarity=0.459 Sum_probs=16.0
Q ss_pred cCCCCCCCCceeEec---CCc-----ceeEe-cccc
Q 043865 115 HGARRPACGSCVERK---EGC-----RVMYC-RCKT 141 (203)
Q Consensus 115 ~~k~CP~C~~~iek~---~GC-----nhm~C-~C~~ 141 (203)
..|+||-|+...... .+= ..+.| .||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 358999998644433 221 45667 4665
No 144
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=47.25 E-value=30 Score=29.04 Aligned_cols=56 Identities=14% Similarity=0.168 Sum_probs=34.9
Q ss_pred HHHHhhcCCHHHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 15 LFTCKLMIPSNLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 15 ~~~i~~~l~~e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
.+.+-..++.+.+..+.+...- +. ....++|| .|+.-...... ..+..|+.|++.+
T Consensus 83 lR~l~~~~~~~~~~~~~~a~~l--~~w~~~~RFCg--~CG~~~~~~~~-----g~~~~C~~cg~~~ 139 (279)
T COG2816 83 LRSLLTELDEGLFGLAARAVQL--LEWYRSHRFCG--RCGTKTYPREG-----GWARVCPKCGHEH 139 (279)
T ss_pred HHHHhccCCHHHHHHHHHHHHH--HHHHhhCcCCC--CCCCcCccccC-----ceeeeCCCCCCcc
Confidence 3333344556666655443322 22 45678999 59987776655 6788999988653
No 145
>PHA02926 zinc finger-like protein; Provisional
Probab=47.16 E-value=9.3 Score=31.00 Aligned_cols=46 Identities=17% Similarity=0.236 Sum_probs=28.9
Q ss_pred HHHHhccCCCCCCCCceeEecCCcceeE--e--cccccccccccccCcCC
Q 043865 109 KLVERMHGARRPACGSCVERKEGCRVMY--C--RCKTSFCYECGGNLKSA 154 (203)
Q Consensus 109 ~~~~~~~~k~CP~C~~~iek~~GCnhm~--C--~C~~~FC~~C~~~~~~~ 154 (203)
+..+...-+.|+=|--.+-+...-+.-+ = .|+|.||+.|-..|...
T Consensus 163 ~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~ 212 (242)
T PHA02926 163 DVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRT 212 (242)
T ss_pred HHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHh
Confidence 3344445588999997663322111111 1 58889999999999863
No 146
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=46.93 E-value=37 Score=18.48 Aligned_cols=17 Identities=18% Similarity=0.225 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHh
Q 043865 179 LIFTVLGVLGGVIYGIY 195 (203)
Q Consensus 179 ~~f~~l~~~~~~~~~~~ 195 (203)
..|++.+.||.+.|.|+
T Consensus 6 Ytfll~~tlgiiFFAIf 22 (31)
T PRK11875 6 YILILTLALVTLFFAIA 22 (31)
T ss_pred HHHHHHHHHHHHHHhhh
Confidence 34555566666666654
No 147
>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=46.87 E-value=38 Score=24.35 Aligned_cols=27 Identities=30% Similarity=0.584 Sum_probs=17.2
Q ss_pred CCceeCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 42 FERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 42 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
+-..+|+ +|+..+..+.. ...||.|+.
T Consensus 68 p~~~~C~--~Cg~~~~~~~~-------~~~CP~Cgs 94 (115)
T TIGR00100 68 PVECECE--DCSEEVSPEID-------LYRCPKCHG 94 (115)
T ss_pred CcEEEcc--cCCCEEecCCc-------CccCcCCcC
Confidence 4557887 58866655432 356887765
No 148
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=46.84 E-value=20 Score=29.81 Aligned_cols=24 Identities=17% Similarity=0.278 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhh
Q 043865 176 GLILIFTVLGVLGGVIYGIYCVIK 199 (203)
Q Consensus 176 ~~~~~f~~l~~~~~~~~~~~~~~~ 199 (203)
..+|++++|++++++|++.|+--+
T Consensus 204 ~wl~i~~~l~~~~Y~i~g~~~n~~ 227 (268)
T PF09451_consen 204 TWLFIILFLFLAAYLIFGSWYNYN 227 (268)
T ss_pred HHHHHHHHHHHHHHhhhhhheeec
Confidence 344555666667777777776443
No 149
>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=46.33 E-value=26 Score=21.75 Aligned_cols=29 Identities=24% Similarity=0.436 Sum_probs=20.1
Q ss_pred eCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 46 YCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 46 ~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
-|| .|+.-+..++. .....+.||.|+..+
T Consensus 4 ~CP--~CG~~iev~~~---~~GeiV~Cp~CGael 32 (54)
T TIGR01206 4 ECP--DCGAEIELENP---ELGELVICDECGAEL 32 (54)
T ss_pred CCC--CCCCEEecCCC---ccCCEEeCCCCCCEE
Confidence 477 69988766554 225578999888764
No 150
>PF15061 DUF4538: Domain of unknown function (DUF4538)
Probab=46.26 E-value=23 Score=22.34 Aligned_cols=17 Identities=29% Similarity=0.727 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHhh
Q 043865 180 IFTVLGVLGGVIYGIYC 196 (203)
Q Consensus 180 ~f~~l~~~~~~~~~~~~ 196 (203)
+--+++++|+.+||||.
T Consensus 11 ~ggfVg~iG~a~Ypi~~ 27 (58)
T PF15061_consen 11 VGGFVGLIGAALYPIYF 27 (58)
T ss_pred HHHHHHHHHHHHhhhhc
Confidence 34466788888999985
No 151
>COG4897 CsbA Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.99 E-value=47 Score=21.88 Aligned_cols=26 Identities=23% Similarity=0.457 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhh
Q 043865 173 IISGLILIFTVLGVLGGVIYGIYCVI 198 (203)
Q Consensus 173 ~~~~~~~~f~~l~~~~~~~~~~~~~~ 198 (203)
+++.+++++++..+++.+-|..|+.+
T Consensus 4 ~~sAlfFPc~LVvLF~riT~n~yVa~ 29 (78)
T COG4897 4 IISALFFPCLLVVLFARITYNRYVAL 29 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46677777877777778888877754
No 152
>PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=45.76 E-value=20 Score=27.69 Aligned_cols=15 Identities=20% Similarity=0.862 Sum_probs=11.1
Q ss_pred ceeEe--cccccccccc
Q 043865 133 RVMYC--RCKTSFCYEC 147 (203)
Q Consensus 133 nhm~C--~C~~~FC~~C 147 (203)
++..| .|...||=.=
T Consensus 25 ~~~~CCG~C~~ryCC~~ 41 (179)
T PF13908_consen 25 DFTFCCGTCSLRYCCSD 41 (179)
T ss_pred CcceecCCccCcchhhh
Confidence 56666 7999998553
No 153
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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 domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=45.55 E-value=3.3 Score=22.50 Aligned_cols=20 Identities=25% Similarity=0.494 Sum_probs=10.8
Q ss_pred ccCCcccCCCcCCHHHHhhc
Q 043865 2 IECPGVHCDQFLDLFTCKLM 21 (203)
Q Consensus 2 I~CP~~~C~~~l~~~~i~~~ 21 (203)
|+||..+|.+.+....-...
T Consensus 3 vrCPvkdC~EEv~lgKY~~H 22 (30)
T PF10426_consen 3 VRCPVKDCDEEVSLGKYSHH 22 (30)
T ss_dssp EE--STT---EEEHHHHHHH
T ss_pred cccccccCcchhhhhhhccc
Confidence 78999999998877655443
No 154
>PF01788 PsbJ: PsbJ; InterPro: IPR002682 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbJ found in PSII. PsbJ is one of the most hydrophobic proteins in the thylakoid membrane, and is located in a gene cluster with PsbE, PsbF and PsbL (PsbEFJL). Both PsbJ and PsbL (IPR003372 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbJ cause the light-harvesting antenna to remain detached from the PSII dimers []. In addition, both PsbJ and PsbL are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_J 3ARC_J 3A0B_J 3KZI_J 2AXT_J 3PRQ_J 4FBY_b 3BZ2_J 1S5L_j 3PRR_J ....
Probab=45.28 E-value=25 Score=20.37 Aligned_cols=16 Identities=38% Similarity=0.870 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHhh
Q 043865 181 FTVLGVLGGVIYGIYC 196 (203)
Q Consensus 181 f~~l~~~~~~~~~~~~ 196 (203)
..++.++|+++|+-|.
T Consensus 19 ~~vi~lvglFfYGsYs 34 (40)
T PF01788_consen 19 IAVIGLVGLFFYGSYS 34 (40)
T ss_dssp HHHHHHHHHHHHCTTT
T ss_pred HHHHHHHHHheecccC
Confidence 5567788888998874
No 155
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.75 E-value=43 Score=24.81 Aligned_cols=35 Identities=14% Similarity=0.072 Sum_probs=21.0
Q ss_pred CHHHHHHHHHHHHHhhcc---------CCCceeCCCCCCCceeeec
Q 043865 23 PSNLFSKWCDVLCEDYVL---------GFERSYCPNRNCMALVVNE 59 (203)
Q Consensus 23 ~~e~~~~y~~~~~~~~i~---------~~~~~~Cp~~~C~~~~~~~ 59 (203)
.++.++..-..+.+..+. .+...+|+ +|+.....+
T Consensus 40 ~pe~L~fafe~l~~gt~~ega~L~i~~~p~~~~C~--~CG~~~~~~ 83 (135)
T PRK03824 40 DKEIVEFALNELLKGTILEGAEIIFEEEEAVLKCR--NCGNEWSLK 83 (135)
T ss_pred hHHHHHHHHHHHHcCCcccCCEEEEEecceEEECC--CCCCEEecc
Confidence 355555555555554332 23568898 699877665
No 156
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=44.69 E-value=5.4 Score=24.22 Aligned_cols=34 Identities=18% Similarity=0.449 Sum_probs=16.4
Q ss_pred CCCCCceeEecCCcceeEecccccccccccccCcC
Q 043865 119 RPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKS 153 (203)
Q Consensus 119 CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~ 153 (203)
||.|-..+ ...|=+..-|.|+++.|..|......
T Consensus 1 cp~C~e~~-d~~d~~~~PC~Cgf~IC~~C~~~i~~ 34 (48)
T PF14570_consen 1 CPLCDEEL-DETDKDFYPCECGFQICRFCYHDILE 34 (48)
T ss_dssp -TTTS-B---CCCTT--SSTTS----HHHHHHHTT
T ss_pred CCCccccc-ccCCCccccCcCCCcHHHHHHHHHHh
Confidence 56666666 33445777788999999998666653
No 157
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=44.57 E-value=25 Score=26.78 Aligned_cols=38 Identities=26% Similarity=0.384 Sum_probs=22.4
Q ss_pred CCceeCCCCCCCcee----eecCccccCCCCceeCCCccccc
Q 043865 42 FERSYCPNRNCMALV----VNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 42 ~~~~~Cp~~~C~~~~----~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
.+.+.||||+|-.-. ...-.+.+......+|..|.+.+
T Consensus 103 ~gi~kC~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~ 144 (152)
T PRK00893 103 EGVLKCPNPNCITNTNEPVESRFYVVDKEPIKLRCKYCEKEF 144 (152)
T ss_pred cceEECCCCCCcCCCCcCcCcEEEEEeCCCCEEEeeCCCCEe
Confidence 467999999995431 00000112346678898887653
No 158
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=44.43 E-value=43 Score=24.00 Aligned_cols=47 Identities=19% Similarity=0.507 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHHHHhhcc---------CCCceeCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 22 IPSNLFSKWCDVLCEDYVL---------GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 22 l~~e~~~~y~~~~~~~~i~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
+.++.++-.-+.+.+..+. .+-..+|+ +|+..+..+.. ...||.|+.
T Consensus 39 v~pe~L~f~f~~~~~~T~~egA~L~I~~vp~~~~C~--~Cg~~~~~~~~-------~~~CP~Cgs 94 (113)
T PRK12380 39 VEESAVRFSFEIVCHGTVAQGCDLHIVYKPAQAWCW--DCSQVVEIHQH-------DAQCPHCHG 94 (113)
T ss_pred cCHHHHHHHHHHHhCCCccCCCEEEEEeeCcEEEcc--cCCCEEecCCc-------CccCcCCCC
Confidence 3455555444444444331 34457887 58866655432 345887764
No 159
>CHL00031 psbT photosystem II protein T
Probab=43.38 E-value=34 Score=18.90 Aligned_cols=17 Identities=24% Similarity=0.667 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHHHh
Q 043865 179 LIFTVLGVLGGVIYGIY 195 (203)
Q Consensus 179 ~~f~~l~~~~~~~~~~~ 195 (203)
..|++.+.||.+.|.|+
T Consensus 6 Ytfll~~tlgilFFAI~ 22 (33)
T CHL00031 6 YTFLLVSTLGIIFFAIF 22 (33)
T ss_pred HHHHHHHHHHHHHHhhe
Confidence 34555566666666654
No 160
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=43.27 E-value=23 Score=26.87 Aligned_cols=38 Identities=24% Similarity=0.381 Sum_probs=21.9
Q ss_pred CCCceeCCCCCCCceeee--cCc--cccCCCCceeCCCcccc
Q 043865 41 GFERSYCPNRNCMALVVN--EGE--INYGTLKKARCPNCKQW 78 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~~~~--~~~--~~~~~~~~~~C~~C~~~ 78 (203)
..++..||||+|-.--.. +.. +.++......|..|.+.
T Consensus 103 i~gvlkCpN~nCITn~e~pv~s~F~~~~~~~~~lrC~YCe~~ 144 (153)
T COG1781 103 IEGVLRCPNPNCITNAEEPVESKFYVVSKEPLALRCKYCEKT 144 (153)
T ss_pred hccEEEcCCCCcccCCCccCCccEEEEecCCcEEEEEecCcE
Confidence 346799999999532210 000 11223567888887765
No 161
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=43.16 E-value=15 Score=22.93 Aligned_cols=10 Identities=30% Similarity=0.707 Sum_probs=5.2
Q ss_pred ceeCCCcccc
Q 043865 69 KARCPNCKQW 78 (203)
Q Consensus 69 ~~~C~~C~~~ 78 (203)
.++||.|++.
T Consensus 21 iVvCp~Cgap 30 (54)
T PF14446_consen 21 IVVCPECGAP 30 (54)
T ss_pred EEECCCCCCc
Confidence 4555555443
No 162
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=42.85 E-value=49 Score=25.96 Aligned_cols=38 Identities=24% Similarity=0.387 Sum_probs=19.1
Q ss_pred CCCceeCCCCCCCc-eeeecCc--cccCCCCceeCCCcccc
Q 043865 41 GFERSYCPNRNCMA-LVVNEGE--INYGTLKKARCPNCKQW 78 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~-~~~~~~~--~~~~~~~~~~C~~C~~~ 78 (203)
..++-.||+-.|++ .+.+-+. ....+..++.||.|+-.
T Consensus 96 ~g~FG~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~dv 136 (184)
T PF01214_consen 96 QGDFGRCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCKDV 136 (184)
T ss_dssp TTTT-B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTTEE
T ss_pred CCcCCcCCcccCCCCceeCccCCCCCCccceeEECCCCccc
Confidence 35677899999996 3333322 12234555666655443
No 163
>KOG1726 consensus HVA22/DP1 gene product-related proteins [Defense mechanisms]
Probab=42.79 E-value=39 Score=27.47 Aligned_cols=33 Identities=15% Similarity=0.161 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcc
Q 043865 170 YCAIISGLILIFTVLGVLGGVIYGIYCVIKRVL 202 (203)
Q Consensus 170 ~~~~~~~~~~~f~~l~~~~~~~~~~~~~~~~~~ 202 (203)
+++|+.+....|=.+.-+.+..+|+|..+|..+
T Consensus 37 ~YWIv~A~~t~~e~~~d~~lsw~P~Y~e~Kl~f 69 (225)
T KOG1726|consen 37 MYWIVFAALTVFETLTDFLLSWFPFYSEFKLAF 69 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence 455555555555555444455999999999765
No 164
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=42.76 E-value=20 Score=30.04 Aligned_cols=24 Identities=29% Similarity=0.757 Sum_probs=18.8
Q ss_pred CCCCCCCceeEec--CCcceeEe-ccc
Q 043865 117 ARRPACGSCVERK--EGCRVMYC-RCK 140 (203)
Q Consensus 117 k~CP~C~~~iek~--~GCnhm~C-~C~ 140 (203)
++|+.|+..|+|. +|=+-..| +|+
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 6999999999987 66666666 464
No 165
>PRK14748 kdpF potassium-transporting ATPase subunit F; Provisional
Probab=42.38 E-value=55 Score=17.49 Aligned_cols=19 Identities=37% Similarity=0.945 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 043865 173 IISGLILIFTVLGVLGGVIYGI 194 (203)
Q Consensus 173 ~~~~~~~~f~~l~~~~~~~~~~ 194 (203)
++.+.++.+ +++|+++|.+
T Consensus 5 vi~G~ilv~---lLlgYLvyAL 23 (29)
T PRK14748 5 VITGVLLVF---LLLGYLVYAL 23 (29)
T ss_pred HHHHHHHHH---HHHHHHHHHH
Confidence 444555444 3444455554
No 166
>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=42.38 E-value=9.3 Score=21.07 Aligned_cols=11 Identities=36% Similarity=0.803 Sum_probs=6.8
Q ss_pred CCCCCCCCcee
Q 043865 116 GARRPACGSCV 126 (203)
Q Consensus 116 ~k~CP~C~~~i 126 (203)
.-+||.|+..|
T Consensus 17 ~irC~~CG~RI 27 (32)
T PF03604_consen 17 PIRCPECGHRI 27 (32)
T ss_dssp TSSBSSSS-SE
T ss_pred cEECCcCCCeE
Confidence 35788887665
No 167
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.20 E-value=20 Score=33.95 Aligned_cols=34 Identities=24% Similarity=0.492 Sum_probs=24.4
Q ss_pred CCCCCCCceeEecCCcceeEe-ccccc----cccccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTS----FCYECGGN 150 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~----FC~~C~~~ 150 (203)
-+||+|.....-..+=+.+.| .||+. .|-.|+..
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 379999988876666678999 69864 35566554
No 168
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=41.56 E-value=17 Score=22.43 Aligned_cols=21 Identities=14% Similarity=0.230 Sum_probs=14.5
Q ss_pred HHHHHHHHhccCCCCCCCCce
Q 043865 105 IAFGKLVERMHGARRPACGSC 125 (203)
Q Consensus 105 ~~~~~~~~~~~~k~CP~C~~~ 125 (203)
..+.++......-.||+|+..
T Consensus 35 ~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 35 QELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHHHHHHcCCCeEECcCCCcc
Confidence 344555555677899999975
No 169
>KOG4007 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.15 E-value=8.9 Score=30.33 Aligned_cols=17 Identities=18% Similarity=0.593 Sum_probs=11.8
Q ss_pred HHHHHHH-HHHHHHhhhh
Q 043865 182 TVLGVLG-GVIYGIYCVI 198 (203)
Q Consensus 182 ~~l~~~~-~~~~~~~~~~ 198 (203)
|++++|| +++|-+|+|+
T Consensus 139 ivi~ii~iL~lYMvfLmc 156 (229)
T KOG4007|consen 139 IVISIIGILLLYMVFLMC 156 (229)
T ss_pred ehHHHHHHHHHHHHHHHh
Confidence 5667777 4588888875
No 170
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=41.05 E-value=16 Score=36.84 Aligned_cols=31 Identities=32% Similarity=0.836 Sum_probs=22.1
Q ss_pred CCCCCCCceeEecCCcceeEe-cccccc-----cccccccCcC
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSF-----CYECGGNLKS 153 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~F-----C~~C~~~~~~ 153 (203)
++||+|+..+... .| .||.+. |-.||.+...
T Consensus 668 rkCPkCG~~t~~~------fCP~CGs~te~vy~CPsCGaev~~ 704 (1337)
T PRK14714 668 RRCPSCGTETYEN------RCPDCGTHTEPVYVCPDCGAEVPP 704 (1337)
T ss_pred EECCCCCCccccc------cCcccCCcCCCceeCccCCCccCC
Confidence 7999999976432 77 588663 7777776543
No 171
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=41.02 E-value=26 Score=28.71 Aligned_cols=61 Identities=16% Similarity=0.197 Sum_probs=37.9
Q ss_pred HHHhhcCCHHHHHHHHHHHHHh-hcc--CCCceeCCCCCCCceeeecCccc-cCCCCceeCCCcccc
Q 043865 16 FTCKLMIPSNLFSKWCDVLCED-YVL--GFERSYCPNRNCMALVVNEGEIN-YGTLKKARCPNCKQW 78 (203)
Q Consensus 16 ~~i~~~l~~e~~~~y~~~~~~~-~i~--~~~~~~Cp~~~C~~~~~~~~~~~-~~~~~~~~C~~C~~~ 78 (203)
+.+..-++++++..|++..... .+- .-+..-|. +|...++...... ......++||.||..
T Consensus 166 ~~L~~~l~~ell~~yeri~~~~kg~gvvpl~g~~C~--GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 166 EELKEKLDPELLSEYERIRKNKKGVGVVPLEGRVCG--GCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred HHHHHhcCHHHHHHHHHHHhcCCCceEEeecCCccc--CCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 3455668999999999988876 331 12234455 5766654332100 124778999999864
No 172
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.85 E-value=23 Score=29.49 Aligned_cols=25 Identities=36% Similarity=0.798 Sum_probs=18.0
Q ss_pred CCCCCCCceeEec--CCcceeEeccccccccccc
Q 043865 117 ARRPACGSCVERK--EGCRVMYCRCKTSFCYECG 148 (203)
Q Consensus 117 k~CP~C~~~iek~--~GCnhm~C~C~~~FC~~C~ 148 (203)
++||+|+..|++. +| -++.||-.|-
T Consensus 236 ~pC~~Cg~~I~~~~~~g-------R~ty~Cp~CQ 262 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGG-------RGTHFCPQCQ 262 (269)
T ss_pred CCCCcCCCeeEEEEECC-------CCcEECCCCc
Confidence 6899999999986 55 3455555553
No 173
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.75 E-value=33 Score=25.28 Aligned_cols=39 Identities=18% Similarity=0.349 Sum_probs=23.7
Q ss_pred CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccc
Q 043865 41 GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCF 81 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 81 (203)
.....+||. |+............+.+...|+.|+..|=.
T Consensus 27 ~~~~~~cP~--C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 27 QITKVNCPR--CKSSNVVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred hcccCcCCC--CCccceeeECCccccccccccCCcCcceee
Confidence 344578984 776653222212234788899998887643
No 174
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=40.47 E-value=26 Score=16.46 Aligned_cols=16 Identities=31% Similarity=0.735 Sum_probs=12.1
Q ss_pred ccccCCcCCCCCCccc
Q 043865 79 FCFQCKVAWHAGYRCE 94 (203)
Q Consensus 79 ~C~~C~~~~H~~~~C~ 94 (203)
.|++|++.-|....|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 4788888888776664
No 175
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=40.45 E-value=14 Score=18.96 Aligned_cols=11 Identities=36% Similarity=0.872 Sum_probs=7.6
Q ss_pred ceeCCCccccc
Q 043865 69 KARCPNCKQWF 79 (203)
Q Consensus 69 ~~~C~~C~~~~ 79 (203)
.+.|+.|+..|
T Consensus 2 l~~C~~CgR~F 12 (25)
T PF13913_consen 2 LVPCPICGRKF 12 (25)
T ss_pred CCcCCCCCCEE
Confidence 35677777765
No 176
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 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 CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=40.28 E-value=17 Score=19.96 Aligned_cols=12 Identities=33% Similarity=0.899 Sum_probs=7.2
Q ss_pred CccCCcccCCCc
Q 043865 1 KIECPGVHCDQF 12 (203)
Q Consensus 1 ~I~CP~~~C~~~ 12 (203)
+.+||.++|+..
T Consensus 1 e~~CPtpGCdg~ 12 (31)
T PF01530_consen 1 ELKCPTPGCDGS 12 (31)
T ss_dssp -TSSSSTT--SC
T ss_pred CCcCCCCCCCcc
Confidence 468999999863
No 177
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=40.05 E-value=16 Score=25.91 Aligned_cols=17 Identities=18% Similarity=0.417 Sum_probs=9.9
Q ss_pred HHHHHHhccCCCCCCCCc
Q 043865 107 FGKLVERMHGARRPACGS 124 (203)
Q Consensus 107 ~~~~~~~~~~k~CP~C~~ 124 (203)
+.+.+++.. -.||.|+-
T Consensus 53 ~~ev~~~~~-W~CP~Crg 69 (105)
T PF10497_consen 53 VEEVLEDPN-WKCPKCRG 69 (105)
T ss_pred HHHHhcCCc-eECCCCCC
Confidence 334443333 46999986
No 178
>PF12428 DUF3675: Protein of unknown function (DUF3675) ; InterPro: IPR022143 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF00097 from PFAM. There are two completely conserved residues (R and L) that may be functionally important.
Probab=39.95 E-value=42 Score=24.40 Aligned_cols=14 Identities=14% Similarity=0.548 Sum_probs=11.7
Q ss_pred HHHHHHHhhhhhhc
Q 043865 188 GGVIYGIYCVIKRV 201 (203)
Q Consensus 188 ~~~~~~~~~~~~~~ 201 (203)
++++.|+|.|.|++
T Consensus 104 aGilLP~Yim~rai 117 (118)
T PF12428_consen 104 AGILLPCYIMARAI 117 (118)
T ss_pred HHHHHHHHHHHhcc
Confidence 35799999999876
No 179
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.80 E-value=24 Score=33.41 Aligned_cols=33 Identities=27% Similarity=0.646 Sum_probs=25.9
Q ss_pred CCCCCCceeEecCCcceeEe-ccccc-----cccccccc
Q 043865 118 RRPACGSCVERKEGCRVMYC-RCKTS-----FCYECGGN 150 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~ 150 (203)
+||+|.....-...=+.++| .||+. .|-.|+..
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCC
Confidence 79999988775555678999 69976 58888765
No 180
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=39.76 E-value=25 Score=29.26 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=11.7
Q ss_pred CCCCCCCceeEec
Q 043865 117 ARRPACGSCVERK 129 (203)
Q Consensus 117 k~CP~C~~~iek~ 129 (203)
++||+|+..|++.
T Consensus 246 ~pC~~Cg~~I~~~ 258 (274)
T PRK01103 246 EPCRRCGTPIEKI 258 (274)
T ss_pred CCCCCCCCeeEEE
Confidence 6899999999986
No 181
>PF05767 Pox_A14: Poxvirus virion envelope protein A14; InterPro: IPR008785 This family consists of several Poxvirus virion envelope protein A14-like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression [].; GO: 0019031 viral envelope
Probab=39.53 E-value=91 Score=21.56 Aligned_cols=23 Identities=30% Similarity=0.567 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 043865 173 IISGLILIFTVLGVLGGVIYGIY 195 (203)
Q Consensus 173 ~~~~~~~~f~~l~~~~~~~~~~~ 195 (203)
.+|..-|++-.+.+||.++|.-|
T Consensus 46 alSii~FI~giil~lG~~i~s~y 68 (92)
T PF05767_consen 46 ALSIICFILGIILTLGIVIFSMY 68 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555566666677777888776
No 182
>TIGR00240 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff.
Probab=39.37 E-value=29 Score=26.36 Aligned_cols=38 Identities=21% Similarity=0.354 Sum_probs=22.0
Q ss_pred CCceeCCCCCCCceeeecCc---cccCCC-CceeCCCccccc
Q 043865 42 FERSYCPNRNCMALVVNEGE---INYGTL-KKARCPNCKQWF 79 (203)
Q Consensus 42 ~~~~~Cp~~~C~~~~~~~~~---~~~~~~-~~~~C~~C~~~~ 79 (203)
.+.+.||||+|-.-..+-.. +.+.+. ...+|..|.+.+
T Consensus 101 ~gi~kC~Np~CIT~~E~v~~~F~v~~~~~~~~lrC~YCe~~~ 142 (150)
T TIGR00240 101 EGVLKCPNPNCISNAEPVSSKFYVRSEEPDIALRCYYCEKEI 142 (150)
T ss_pred eeeEECCCCCCccCCCCCCcEEEEecCCCceEEEEECCCCEE
Confidence 46799999999643211100 011122 578898887653
No 183
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.03 E-value=28 Score=34.36 Aligned_cols=33 Identities=27% Similarity=0.568 Sum_probs=26.6
Q ss_pred cCCCCCCCCceeEecCCcceeEe-cccc-----cccccccccCcC
Q 043865 115 HGARRPACGSCVERKEGCRVMYC-RCKT-----SFCYECGGNLKS 153 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C-~C~~-----~FC~~C~~~~~~ 153 (203)
..+.||.|+... ....| .||. .||-.|+..-..
T Consensus 625 g~RfCpsCG~~t------~~frCP~CG~~Te~i~fCP~CG~~~~~ 663 (1121)
T PRK04023 625 GRRKCPSCGKET------FYRRCPFCGTHTEPVYRCPRCGIEVEE 663 (1121)
T ss_pred cCccCCCCCCcC------CcccCCCCCCCCCcceeCccccCcCCC
Confidence 458999999985 56789 6985 499999888764
No 184
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=38.83 E-value=41 Score=21.34 Aligned_cols=30 Identities=23% Similarity=0.438 Sum_probs=19.8
Q ss_pred eeCCCCCCCceeeecCccccCCCCceeCCCcccccc
Q 043865 45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFC 80 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C 80 (203)
+.|| +|.+.-..=.. ....+.|..|+...+
T Consensus 12 VkCp--~C~n~q~vFsh----a~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 12 VKCP--DCGNEQVVFSH----ASTVVRCLVCGKTLA 41 (59)
T ss_pred EECC--CCCCeEEEEec----CCcEEECcccCCCcc
Confidence 6787 68876543332 256788888887654
No 185
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=38.34 E-value=22 Score=28.03 Aligned_cols=23 Identities=22% Similarity=0.551 Sum_probs=19.3
Q ss_pred CCCCCCCceeEecCCcceeEe-cccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKT 141 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~ 141 (203)
-+|++|+...++ .=+.|+| +||.
T Consensus 150 A~CsrC~~~L~~--~~~~l~Cp~Cg~ 173 (188)
T COG1096 150 ARCSRCRAPLVK--KGNMLKCPNCGN 173 (188)
T ss_pred EEccCCCcceEE--cCcEEECCCCCC
Confidence 489999999999 4478899 7885
No 186
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=38.32 E-value=6 Score=37.28 Aligned_cols=13 Identities=15% Similarity=0.506 Sum_probs=9.7
Q ss_pred ccCCCCCCCCcee
Q 043865 114 MHGARRPACGSCV 126 (203)
Q Consensus 114 ~~~k~CP~C~~~i 126 (203)
..-++||+|+...
T Consensus 676 tRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 676 TRQRKCPKCNAAF 688 (698)
T ss_pred HhcCCCCCCCCCC
Confidence 3448899998765
No 187
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=38.17 E-value=18 Score=22.00 Aligned_cols=13 Identities=46% Similarity=0.838 Sum_probs=8.1
Q ss_pred cCCCCCCCCceeE
Q 043865 115 HGARRPACGSCVE 127 (203)
Q Consensus 115 ~~k~CP~C~~~ie 127 (203)
..-+||.|+.-|-
T Consensus 23 ~~irCp~Cg~rIl 35 (49)
T COG1996 23 RGIRCPYCGSRIL 35 (49)
T ss_pred CceeCCCCCcEEE
Confidence 3356777776653
No 188
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=38.10 E-value=40 Score=18.38 Aligned_cols=24 Identities=21% Similarity=0.466 Sum_probs=18.5
Q ss_pred CCCCCCceeEecCCcceeEe-cccc
Q 043865 118 RRPACGSCVERKEGCRVMYC-RCKT 141 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C-~C~~ 141 (203)
.|..|+....--.|=..+.| .|++
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCe
Confidence 57888888888888888888 5753
No 189
>PLN02195 cellulose synthase A
Probab=37.97 E-value=22 Score=34.99 Aligned_cols=21 Identities=19% Similarity=0.414 Sum_probs=17.6
Q ss_pred CCCCceeCCCccccccccCCc
Q 043865 65 GTLKKARCPNCKQWFCFQCKV 85 (203)
Q Consensus 65 ~~~~~~~C~~C~~~~C~~C~~ 85 (203)
++...+.|..|+.-.|.-|..
T Consensus 21 ~g~~fvaC~eC~~pvCrpCye 41 (977)
T PLN02195 21 NGEAFVACHECSYPLCKACLE 41 (977)
T ss_pred CCCeEEEeccCCCccccchhh
Confidence 357889999999999988873
No 190
>PRK11827 hypothetical protein; Provisional
Probab=37.88 E-value=29 Score=22.10 Aligned_cols=27 Identities=11% Similarity=0.151 Sum_probs=19.7
Q ss_pred CCCCCCCCceeEecCCcceeEe-ccccc
Q 043865 116 GARRPACGSCVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 142 (203)
+-.||.|+...+-..+=+...| .|+--
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~la 35 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLA 35 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCee
Confidence 3579999998887766667777 56643
No 191
>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=37.66 E-value=19 Score=20.26 Aligned_cols=14 Identities=43% Similarity=0.593 Sum_probs=11.1
Q ss_pred CCCCCCCCceeEec
Q 043865 116 GARRPACGSCVERK 129 (203)
Q Consensus 116 ~k~CP~C~~~iek~ 129 (203)
...||.|+..++|.
T Consensus 26 ~~~CP~Cg~~~~r~ 39 (41)
T smart00834 26 LATCPECGGDVRRL 39 (41)
T ss_pred CCCCCCCCCcceec
Confidence 46799999987764
No 192
>PRK10445 endonuclease VIII; Provisional
Probab=37.63 E-value=27 Score=28.88 Aligned_cols=21 Identities=19% Similarity=0.572 Sum_probs=15.0
Q ss_pred CCCCCCCceeEec--CCcceeEe
Q 043865 117 ARRPACGSCVERK--EGCRVMYC 137 (203)
Q Consensus 117 k~CP~C~~~iek~--~GCnhm~C 137 (203)
++||+|+..|++. +|=.-..|
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~C 258 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWC 258 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEEC
Confidence 7899999999976 55333333
No 193
>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=37.03 E-value=38 Score=19.57 Aligned_cols=28 Identities=21% Similarity=0.415 Sum_probs=17.2
Q ss_pred eCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 46 YCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 46 ~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
.|+ +|+..+.....+.+ .....||.|+.
T Consensus 7 ~C~--~Cg~~fe~~~~~~~--~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCE--ECGHEFEVLQSISE--DDPVPCPECGS 34 (42)
T ss_pred EeC--CCCCEEEEEEEcCC--CCCCcCCCCCC
Confidence 465 68866654333221 56788888876
No 194
>PF15052 TMEM169: TMEM169 protein family
Probab=36.99 E-value=44 Score=24.57 Aligned_cols=38 Identities=24% Similarity=0.350 Sum_probs=27.2
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 043865 164 DVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRV 201 (203)
Q Consensus 164 ~~~~~~~~~~~~~~~~~f~~l~~~~~~~~~~~~~~~~~ 201 (203)
+...-.+..+=..+|++|.+|+++-.+-.++|-.++.+
T Consensus 53 ers~~hKi~~cPlLIl~YP~lIv~~t~~LglYaa~~Ql 90 (133)
T PF15052_consen 53 ERSFWHKITVCPLLILFYPFLIVLVTLSLGLYAAFVQL 90 (133)
T ss_pred cceeeeeehhccHHHHHHHHHHHHHHHHHHHHHHhhhe
Confidence 33344556666678899999988888888888777654
No 195
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=36.81 E-value=33 Score=28.84 Aligned_cols=30 Identities=20% Similarity=0.365 Sum_probs=25.7
Q ss_pred ccCCCCCCCCceeEecCCcceeEe-cccccc
Q 043865 114 MHGARRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 114 ~~~k~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
...|-||+|+...+-.+|=-.+.| .|++.+
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCcc
Confidence 356899999999999999899999 788765
No 196
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.78 E-value=28 Score=28.95 Aligned_cols=13 Identities=15% Similarity=0.248 Sum_probs=11.9
Q ss_pred CCCCCCCceeEec
Q 043865 117 ARRPACGSCVERK 129 (203)
Q Consensus 117 k~CP~C~~~iek~ 129 (203)
++||+|+..|++.
T Consensus 245 ~pCprCG~~I~~~ 257 (272)
T PRK14810 245 EPCLNCKTPIRRV 257 (272)
T ss_pred CcCCCCCCeeEEE
Confidence 6999999999986
No 197
>PRK00523 hypothetical protein; Provisional
Probab=36.72 E-value=67 Score=21.23 Aligned_cols=14 Identities=21% Similarity=0.268 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHhhh
Q 043865 184 LGVLGGVIYGIYCV 197 (203)
Q Consensus 184 l~~~~~~~~~~~~~ 197 (203)
+.+|++++-++|..
T Consensus 13 ~~li~G~~~Gffia 26 (72)
T PRK00523 13 PLLIVGGIIGYFVS 26 (72)
T ss_pred HHHHHHHHHHHHHH
Confidence 33444555555554
No 198
>PF15616 TerY-C: TerY-C metal binding domain
Probab=36.39 E-value=21 Score=26.48 Aligned_cols=26 Identities=27% Similarity=0.721 Sum_probs=17.6
Q ss_pred cCCCCCCCCceeEecCCcceeEeccccccccc
Q 043865 115 HGARRPACGSCVERKEGCRVMYCRCKTSFCYE 146 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~ 146 (203)
+.--||.|+...- ...|.||.-|||.
T Consensus 76 g~PgCP~CGn~~~------fa~C~CGkl~Ci~ 101 (131)
T PF15616_consen 76 GAPGCPHCGNQYA------FAVCGCGKLFCID 101 (131)
T ss_pred CCCCCCCCcChhc------EEEecCCCEEEeC
Confidence 3467999999852 4555666666663
No 199
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=36.32 E-value=66 Score=26.52 Aligned_cols=32 Identities=16% Similarity=0.415 Sum_probs=22.9
Q ss_pred CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 41 GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
..+..||| .|+..+..... .....|+.|+...
T Consensus 96 ~~~~~fC~--~CG~~~~~~~~-----~~~~~C~~c~~~~ 127 (256)
T PRK00241 96 YRSHRFCG--YCGHPMHPSKT-----EWAMLCPHCRERY 127 (256)
T ss_pred hhcCcccc--ccCCCCeecCC-----ceeEECCCCCCEE
Confidence 56789999 59887665443 5667899888654
No 200
>PF04277 OAD_gamma: Oxaloacetate decarboxylase, gamma chain ; InterPro: IPR005899 This family comprises distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit [].; GO: 0008948 oxaloacetate decarboxylase activity, 0015081 sodium ion transmembrane transporter activity, 0071436 sodium ion export, 0016020 membrane
Probab=36.31 E-value=78 Score=20.68 Aligned_cols=21 Identities=38% Similarity=0.352 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 043865 174 ISGLILIFTVLGVLGGVIYGI 194 (203)
Q Consensus 174 ~~~~~~~f~~l~~~~~~~~~~ 194 (203)
++++..-|++|.+|.+++..+
T Consensus 9 i~Gm~iVF~~L~lL~~~i~l~ 29 (79)
T PF04277_consen 9 IIGMGIVFLVLILLILVISLM 29 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334444466666555544433
No 201
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.30 E-value=41 Score=24.77 Aligned_cols=50 Identities=22% Similarity=0.456 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHHhhccCCCceeCCCCCCCceeeecCccc------cCCCCceeCCCccccc
Q 043865 23 PSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEIN------YGTLKKARCPNCKQWF 79 (203)
Q Consensus 23 ~~e~~~~y~~~~~~~~i~~~~~~~Cp~~~C~~~~~~~~~~~------~~~~~~~~C~~C~~~~ 79 (203)
++|+.+.|-...-++.| ..|| .|+..+..+..++ .+......|..|+..|
T Consensus 23 ~pel~eafcskcgeati-----~qcp--~csasirgd~~vegvlglg~dye~psfchncgs~f 78 (160)
T COG4306 23 SPELMEAFCSKCGEATI-----TQCP--ICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRF 78 (160)
T ss_pred CHHHHHHHHhhhchHHH-----hcCC--ccCCcccccceeeeeeccCCCCCCcchhhcCCCCC
Confidence 57888888777777654 4687 5888776554432 2334555666666643
No 202
>COG3296 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.29 E-value=80 Score=23.42 Aligned_cols=16 Identities=13% Similarity=0.137 Sum_probs=8.8
Q ss_pred HHHHHHHHHHhhhhhh
Q 043865 185 GVLGGVIYGIYCVIKR 200 (203)
Q Consensus 185 ~~~~~~~~~~~~~~~~ 200 (203)
+++++.+|++.++|.+
T Consensus 108 ~~~alsi~~lv~ti~a 123 (143)
T COG3296 108 SIFALSILSLVLTIIA 123 (143)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444456666666543
No 203
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=36.09 E-value=16 Score=27.32 Aligned_cols=24 Identities=29% Similarity=0.754 Sum_probs=17.0
Q ss_pred CCCCCCCceeEecCCcceeEecccccccccccccCc
Q 043865 117 ARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLK 152 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~ 152 (203)
-+|.+||.+|. .-.||-.|...+.
T Consensus 82 ~~CE~CG~~I~------------~Gr~C~~C~~~l~ 105 (137)
T TIGR03826 82 YPCERCGTSIR------------EGRLCDSCAGELK 105 (137)
T ss_pred CcccccCCcCC------------CCCccHHHHHHHH
Confidence 57888888885 2367777766544
No 204
>PRK04023 DNA polymerase II large subunit; Validated
Probab=36.05 E-value=34 Score=33.89 Aligned_cols=20 Identities=30% Similarity=0.830 Sum_probs=11.0
Q ss_pred ceeCCCccc-----cccccCCcCCC
Q 043865 69 KARCPNCKQ-----WFCFQCKVAWH 88 (203)
Q Consensus 69 ~~~C~~C~~-----~~C~~C~~~~H 88 (203)
...||.||. .+|-.|+....
T Consensus 638 ~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 638 YRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cccCCCCCCCCCcceeCccccCcCC
Confidence 356666664 35666654433
No 205
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=35.99 E-value=65 Score=23.59 Aligned_cols=20 Identities=30% Similarity=0.665 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHhhh
Q 043865 178 ILIFTVLGVLGGVIYGIYCV 197 (203)
Q Consensus 178 ~~~f~~l~~~~~~~~~~~~~ 197 (203)
|.+-.+.+++|.+++.+|++
T Consensus 69 Ii~gv~aGvIg~Illi~y~i 88 (122)
T PF01102_consen 69 IIFGVMAGVIGIILLISYCI 88 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHH
Confidence 33344445555444444444
No 206
>PF05434 Tmemb_9: TMEM9; InterPro: IPR008853 This family contains several eukaryotic transmembrane proteins which are homologous to Homo sapiens transmembrane protein 9 Q9P0T7 from SWISSPROT. The TMEM9 gene encodes a 183 amino-acid protein that contains an N-terminal signal peptide, a single transmembrane region, three potential N-glycosylation sites and three conserved cys-rich domains in the N terminus, but no known functional domains. The protein is highly conserved between species from Caenorhabditis elegans to H. sapiens and belongs to a novel family of transmembrane proteins. The exact function of TMEM9 is unknown although it has been found to be widely expressed and localised to the late endosomes and lysosomes []. Members of this family contain CXCXC repeats IPR004153 from INTERPRO in their N-terminal region.; GO: 0016021 integral to membrane
Probab=35.94 E-value=23 Score=26.84 Aligned_cols=16 Identities=38% Similarity=0.609 Sum_probs=8.3
Q ss_pred HHHHHH-HHHHHHhhhh
Q 043865 183 VLGVLG-GVIYGIYCVI 198 (203)
Q Consensus 183 ~l~~~~-~~~~~~~~~~ 198 (203)
+|.+|| +++|-+|+++
T Consensus 61 vl~Vi~lLvlYM~fL~~ 77 (149)
T PF05434_consen 61 VLWVIGLLVLYMLFLMC 77 (149)
T ss_pred eHHHHHHHHHHHHHHHH
Confidence 344444 3466666654
No 207
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.86 E-value=14 Score=32.02 Aligned_cols=17 Identities=41% Similarity=1.261 Sum_probs=15.0
Q ss_pred CCccccccccCCcCCCC
Q 043865 73 PNCKQWFCFQCKVAWHA 89 (203)
Q Consensus 73 ~~C~~~~C~~C~~~~H~ 89 (203)
|.|.+.||.+|...|+.
T Consensus 185 pnC~H~~Cl~Cir~wr~ 201 (344)
T KOG1039|consen 185 PNCNHSFCLNCIRKWRQ 201 (344)
T ss_pred CCcchhhhhcHhHhhhh
Confidence 67999999999999973
No 208
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=35.72 E-value=16 Score=21.25 Aligned_cols=33 Identities=21% Similarity=0.361 Sum_probs=22.1
Q ss_pred CCCCCCceeEecCCcceeEecccccccccccccCc
Q 043865 118 RRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLK 152 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~ 152 (203)
.||.|......+.. -+.=.||+.||..|...+.
T Consensus 1 ~C~~C~~~~~~~~~--~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 1 HCNICFEKYSEERR--PRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCcCcCccccCCCC--eEEcccCCHHHHHHHHhhc
Confidence 37778777732222 1111689999999988877
No 209
>TIGR01195 oadG_fam sodium pump decarboxylases, gamma subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins.
Probab=35.71 E-value=82 Score=21.22 Aligned_cols=20 Identities=25% Similarity=0.446 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 043865 175 SGLILIFTVLGVLGGVIYGI 194 (203)
Q Consensus 175 ~~~~~~f~~l~~~~~~~~~~ 194 (203)
.++-+-|++|++|.+++..+
T Consensus 13 ~GM~~VF~fL~lLi~~i~~~ 32 (82)
T TIGR01195 13 LGMGIVFLFLSLLIYAVRGM 32 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444456665554444333
No 210
>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=35.70 E-value=26 Score=17.92 Aligned_cols=13 Identities=38% Similarity=0.861 Sum_probs=9.5
Q ss_pred CCceeCCCccccc
Q 043865 67 LKKARCPNCKQWF 79 (203)
Q Consensus 67 ~~~~~C~~C~~~~ 79 (203)
.....|+.|++.|
T Consensus 12 ~k~~~C~~C~k~F 24 (26)
T PF13465_consen 12 EKPYKCPYCGKSF 24 (26)
T ss_dssp SSSEEESSSSEEE
T ss_pred CCCCCCCCCcCee
Confidence 4568888888765
No 211
>PHA02692 hypothetical protein; Provisional
Probab=35.07 E-value=79 Score=20.72 Aligned_cols=19 Identities=21% Similarity=0.307 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q 043865 177 LILIFTVLGVLGGVIYGIY 195 (203)
Q Consensus 177 ~~~~f~~l~~~~~~~~~~~ 195 (203)
.+++|++..+++.++..+|
T Consensus 48 ~ii~~~~~~~~~vll~flY 66 (70)
T PHA02692 48 VFLIGLIAAAIGVLLCFHY 66 (70)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444
No 212
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.05 E-value=31 Score=28.70 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=11.9
Q ss_pred CCCCCCCceeEec
Q 043865 117 ARRPACGSCVERK 129 (203)
Q Consensus 117 k~CP~C~~~iek~ 129 (203)
++||+|+..|++.
T Consensus 246 ~pC~~Cg~~I~~~ 258 (272)
T TIGR00577 246 EPCRRCGTPIEKI 258 (272)
T ss_pred CCCCCCCCeeEEE
Confidence 6999999999986
No 213
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=34.88 E-value=32 Score=21.79 Aligned_cols=32 Identities=19% Similarity=0.414 Sum_probs=21.6
Q ss_pred CCceeCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 42 FERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 42 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
..+=.|-+.+|++++..+-. ....-.||-|+.
T Consensus 16 t~VW~Ct~e~C~gWmR~nFs----~~~~p~CPlC~s 47 (59)
T PF14169_consen 16 TKVWECTSEDCNGWMRDNFS----FEEEPVCPLCKS 47 (59)
T ss_pred eeeEEeCCCCCCcccccccc----cCCCccCCCcCC
Confidence 34567999999999986554 233356776654
No 214
>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=34.85 E-value=29 Score=24.93 Aligned_cols=20 Identities=35% Similarity=0.753 Sum_probs=14.2
Q ss_pred ceeEecccccccccccccCcC
Q 043865 133 RVMYCRCKTSFCYECGGNLKS 153 (203)
Q Consensus 133 nhm~C~C~~~FC~~C~~~~~~ 153 (203)
..+.|.||++||-. ...|+.
T Consensus 23 k~vkc~CGh~f~d~-r~NwK~ 42 (112)
T PF08882_consen 23 KVVKCDCGHEFCDA-RENWKL 42 (112)
T ss_pred ceeeccCCCeecCh-hcChhh
Confidence 47899999999854 334443
No 215
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=34.80 E-value=46 Score=24.62 Aligned_cols=24 Identities=17% Similarity=0.267 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhh
Q 043865 177 LILIFTVLGVLGGVIYGIYCVIKR 200 (203)
Q Consensus 177 ~~~~f~~l~~~~~~~~~~~~~~~~ 200 (203)
.|+.+.+++++.+++|.+|...|+
T Consensus 105 ~il~il~~i~is~~~~~~yr~~r~ 128 (139)
T PHA03099 105 GIVLVLVGIIITCCLLSVYRFTRR 128 (139)
T ss_pred HHHHHHHHHHHHHHHHhhheeeec
Confidence 455666677777888999988876
No 216
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=34.70 E-value=19 Score=22.87 Aligned_cols=38 Identities=26% Similarity=0.538 Sum_probs=29.7
Q ss_pred CCCCCCCceeEe--cCCcceeEe-cccccccccccccCcCC
Q 043865 117 ARRPACGSCVER--KEGCRVMYC-RCKTSFCYECGGNLKSA 154 (203)
Q Consensus 117 k~CP~C~~~iek--~~GCnhm~C-~C~~~FC~~C~~~~~~~ 154 (203)
..||-|+....- .+-=|+=+| .|+.+-|-.||-.-.+|
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlCGFNP~Ph 43 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLCGFNPTPH 43 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhcccCCCCCcc
Confidence 468999886622 245799999 79999999999887654
No 217
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=34.42 E-value=55 Score=19.92 Aligned_cols=21 Identities=43% Similarity=0.778 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHhhhhhhc
Q 043865 181 FTVLGVLGGVIYGIYCVIKRV 201 (203)
Q Consensus 181 f~~l~~~~~~~~~~~~~~~~~ 201 (203)
|+++.++.+++.++|.++|.+
T Consensus 34 ~~~~g~llG~~~g~~~~~~~~ 54 (55)
T PF09527_consen 34 FTLIGLLLGIAAGFYNVYRLV 54 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 444455556667777777653
No 218
>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=34.39 E-value=62 Score=26.38 Aligned_cols=28 Identities=14% Similarity=0.292 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 043865 173 IISGLILIFTVLGVLGGVIYGIYCVIKR 200 (203)
Q Consensus 173 ~~~~~~~~f~~l~~~~~~~~~~~~~~~~ 200 (203)
+|+..++..+++.++..++.|+|-|+.+
T Consensus 189 vilpvvIaliVitl~vf~LvgLyr~C~k 216 (259)
T PF07010_consen 189 VILPVVIALIVITLSVFTLVGLYRMCWK 216 (259)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3433444445555555668899988764
No 219
>PF06716 DUF1201: Protein of unknown function (DUF1201); InterPro: IPR009591 This entry consists of several Beet yellows virus (BYV) putative membrane-binding proteins of around 54 residues in length. The function of this currently unknown.
Probab=34.31 E-value=1.1e+02 Score=18.43 Aligned_cols=15 Identities=33% Similarity=0.565 Sum_probs=9.6
Q ss_pred HHHHHHhhhhhhccC
Q 043865 189 GVIYGIYCVIKRVLF 203 (203)
Q Consensus 189 ~~~~~~~~~~~~~~~ 203 (203)
+++|.|+.+-|..||
T Consensus 23 ~~~~F~~F~~Kqilf 37 (54)
T PF06716_consen 23 CLVVFIWFVYKQILF 37 (54)
T ss_pred HHHHHHHHHHHHHHH
Confidence 446667777776654
No 220
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=34.24 E-value=35 Score=24.41 Aligned_cols=48 Identities=21% Similarity=0.340 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHHHhhcc---------CCCceeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 22 IPSNLFSKWCDVLCEDYVL---------GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 22 l~~e~~~~y~~~~~~~~i~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
+.++.++-.-+.+.+..+. .|-..+|. +|+.-+..+.. ...||.|+..
T Consensus 39 V~pe~L~f~f~~~~~~T~~e~a~L~Ie~~p~~~~C~--~Cg~~~~~~~~-------~~~CP~Cgs~ 95 (113)
T PF01155_consen 39 VEPEALRFAFEVLAEGTILEGAELEIEEVPARARCR--DCGHEFEPDEF-------DFSCPRCGSP 95 (113)
T ss_dssp --HHHHHHHHHHHHCCSTTTT-EEEEEEE--EEEET--TTS-EEECHHC-------CHH-SSSSSS
T ss_pred CCHHHHHHHHHHHhCCCCccCCEEEEEecCCcEECC--CCCCEEecCCC-------CCCCcCCcCC
Confidence 4566665555555554332 23457777 58877766554 2567777653
No 221
>PRK13183 psbN photosystem II reaction center protein N; Provisional
Probab=34.20 E-value=36 Score=20.41 Aligned_cols=19 Identities=26% Similarity=0.331 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q 043865 180 IFTVLGVLGGVIYGIYCVI 198 (203)
Q Consensus 180 ~f~~l~~~~~~~~~~~~~~ 198 (203)
+|+...++++.-|++|..+
T Consensus 12 i~i~~lL~~~TgyaiYtaF 30 (46)
T PRK13183 12 ITILAILLALTGFGIYTAF 30 (46)
T ss_pred HHHHHHHHHHhhheeeecc
Confidence 3555555555667777544
No 222
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=34.07 E-value=1.1e+02 Score=21.75 Aligned_cols=49 Identities=20% Similarity=0.387 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCc
Q 043865 22 IPSNLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKV 85 (203)
Q Consensus 22 l~~e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~ 85 (203)
+++...+..++++.=.... ......|++ |+..-. ...+|+..+|.+|+.
T Consensus 19 l~~~~~k~~~~il~Crt~~~G~~~~~C~~--Cg~~~~-------------~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 19 LSPYQRKAVEAILACRTEALGFHRYRCED--CGHEKI-------------VYNSCKNRHCPSCQA 68 (111)
T ss_pred CCHHHHHHHHHHHhcCCccCCcceeecCC--CCceEE-------------ecCcccCcCCCCCCC
Confidence 5555555555554443332 445566763 765433 333578888877764
No 223
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.04 E-value=32 Score=28.82 Aligned_cols=21 Identities=29% Similarity=0.627 Sum_probs=15.3
Q ss_pred CCCCCCCceeEec--CCcceeEe
Q 043865 117 ARRPACGSCVERK--EGCRVMYC 137 (203)
Q Consensus 117 k~CP~C~~~iek~--~GCnhm~C 137 (203)
++||+|+..|++. +|=.-..|
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~C 277 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWC 277 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEEC
Confidence 6999999999986 55333334
No 224
>PF14369 zf-RING_3: zinc-finger
Probab=33.99 E-value=62 Score=18.04 Aligned_cols=29 Identities=24% Similarity=0.586 Sum_probs=17.0
Q ss_pred eeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865 45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF 79 (203)
Q Consensus 45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~ 79 (203)
.||= .|+..+..... ....+.||.|+..|
T Consensus 3 ywCh--~C~~~V~~~~~----~~~~~~CP~C~~gF 31 (35)
T PF14369_consen 3 YWCH--QCNRFVRIAPS----PDSDVACPRCHGGF 31 (35)
T ss_pred EeCc--cCCCEeEeCcC----CCCCcCCcCCCCcE
Confidence 4665 58877776433 12234688887644
No 225
>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=33.67 E-value=72 Score=29.07 Aligned_cols=62 Identities=21% Similarity=0.351 Sum_probs=37.6
Q ss_pred hcCCHHHHHHHHHHHHHh--hcc-CC-----CceeCCC-------CCCCceeeecCccccCCCCceeCCCcccc-----c
Q 043865 20 LMIPSNLFSKWCDVLCED--YVL-GF-----ERSYCPN-------RNCMALVVNEGEINYGTLKKARCPNCKQW-----F 79 (203)
Q Consensus 20 ~~l~~e~~~~y~~~~~~~--~i~-~~-----~~~~Cp~-------~~C~~~~~~~~~~~~~~~~~~~C~~C~~~-----~ 79 (203)
..+++++++...+.+.+. .+. .+ ..+.|.. |+|+..+..... .....|+.|++. .
T Consensus 181 ~~ls~~l~~~i~~~l~~g~qvLvflnrrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~-----~~~l~Ch~Cg~~~~~~~~ 255 (505)
T TIGR00595 181 SFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKK-----EGKLRCHYCGYQEPIPKT 255 (505)
T ss_pred CCccHHHHHHHHHHHHcCCcEEEEEeCCcCCCeeEhhhCcCccCCCCCCCceEEecC-----CCeEEcCCCcCcCCCCCC
Confidence 356777787777776553 121 11 1234431 257766665544 567899999877 4
Q ss_pred cccCCcC
Q 043865 80 CFQCKVA 86 (203)
Q Consensus 80 C~~C~~~ 86 (203)
|-.|...
T Consensus 256 Cp~C~s~ 262 (505)
T TIGR00595 256 CPQCGSE 262 (505)
T ss_pred CCCCCCC
Confidence 8888764
No 226
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=33.49 E-value=25 Score=29.41 Aligned_cols=34 Identities=38% Similarity=0.821 Sum_probs=15.6
Q ss_pred CCCCCCCce-----eEecC--CcceeEe-cccccc------ccccccc
Q 043865 117 ARRPACGSC-----VERKE--GCRVMYC-RCKTSF------CYECGGN 150 (203)
Q Consensus 117 k~CP~C~~~-----iek~~--GCnhm~C-~C~~~F------C~~C~~~ 150 (203)
..||-||.. +...+ |=-+++| .|+++| |-.||..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNT 220 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCC
Confidence 689999985 33334 7888999 798877 5677665
No 228
>PF12459 DUF3687: D-Ala-teichoic acid biosynthesis protein; InterPro: IPR021008 Proteins in this family are bacterial proteins of approximately 50 amino acids in length. There are two completely conserved residues (L and Y) that may be functionally important. A number of entries are annotated as D-Ala-teichoic acid biosynthesis protein; however there is no direct evidence to support this annotation.
Probab=33.02 E-value=1.1e+02 Score=18.03 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 043865 171 CAIISGLILIFTVLGVLGGVIYG 193 (203)
Q Consensus 171 ~~~~~~~~~~f~~l~~~~~~~~~ 193 (203)
...|++..++|+++.++++-+|+
T Consensus 7 ~~~fi~~T~fYf~Ill~L~ylYg 29 (42)
T PF12459_consen 7 AVKFIGKTLFYFAILLALIYLYG 29 (42)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34566777776666555555554
No 229
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=32.90 E-value=32 Score=26.87 Aligned_cols=24 Identities=17% Similarity=0.404 Sum_probs=19.9
Q ss_pred CCCCCCceeEecCCcceeEe-ccccc
Q 043865 118 RRPACGSCVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C-~C~~~ 142 (203)
+|+.|+.+..+.+. |.|.| .|++.
T Consensus 151 ~~~~~g~~~~~~~~-~~~~c~~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVKKGE-NELKCPNCGNI 175 (189)
T ss_pred EccccCCceEECCC-CEEECCCCCCE
Confidence 69999999988544 99999 79864
No 230
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=32.85 E-value=60 Score=20.26 Aligned_cols=32 Identities=16% Similarity=0.402 Sum_probs=18.3
Q ss_pred ceeCCCCCCCceeeecCccccCCCCceeCCCccccccc
Q 043865 44 RSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCF 81 (203)
Q Consensus 44 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~ 81 (203)
.+.|| +|.+.-..=.. ....+.|..|+...|.
T Consensus 7 ~VkCp--~C~~~q~vFSh----a~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 7 DVKCP--GCYNIQTVFSH----AQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EEE-T--TT-SEEEEETT-----SS-EE-SSSTSEEEE
T ss_pred EEECC--CCCCeeEEEec----CCeEEEcccCCCEecC
Confidence 36787 68876544332 3678999999888764
No 231
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=32.70 E-value=30 Score=28.53 Aligned_cols=28 Identities=18% Similarity=0.364 Sum_probs=22.4
Q ss_pred cCCCCCCCCceeEecCCcceeEe-ccccc
Q 043865 115 HGARRPACGSCVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~ 142 (203)
..+-||.|+...+...+=..+.| .|+..
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCE
Confidence 45899999999887766677889 78853
No 232
>PRK01844 hypothetical protein; Provisional
Probab=32.65 E-value=86 Score=20.72 Aligned_cols=15 Identities=20% Similarity=0.554 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHhhhh
Q 043865 184 LGVLGGVIYGIYCVI 198 (203)
Q Consensus 184 l~~~~~~~~~~~~~~ 198 (203)
+.+|++++-++|..-
T Consensus 12 ~~li~G~~~Gff~ar 26 (72)
T PRK01844 12 VALVAGVALGFFIAR 26 (72)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344445555555543
No 233
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=32.36 E-value=1e+02 Score=17.55 Aligned_cols=21 Identities=19% Similarity=0.263 Sum_probs=9.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHH
Q 043865 169 HYCAIISGLILIFTVLGVLGG 189 (203)
Q Consensus 169 ~~~~~~~~~~~~f~~l~~~~~ 189 (203)
++=+++-++.++++|+.++|+
T Consensus 13 Er~Wi~F~l~mi~vFi~li~y 33 (38)
T PF09125_consen 13 ERGWIAFALAMILVFIALIGY 33 (38)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHHHHHHHHHH
Confidence 333444344444444455543
No 234
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=32.30 E-value=37 Score=20.13 Aligned_cols=14 Identities=21% Similarity=0.489 Sum_probs=10.4
Q ss_pred cCCCCCCCCceeEe
Q 043865 115 HGARRPACGSCVER 128 (203)
Q Consensus 115 ~~k~CP~C~~~iek 128 (203)
..+.||-|+..|++
T Consensus 36 ~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 36 RKKKCPICRQPIES 49 (50)
T ss_dssp TTSBBTTTTBB-SE
T ss_pred cCCCCCcCChhhcC
Confidence 44789999999875
No 235
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=32.16 E-value=86 Score=25.96 Aligned_cols=37 Identities=24% Similarity=0.436 Sum_probs=21.1
Q ss_pred CCCceeCCCCCCCce-eeecCc--cccCCCCceeCCCccc
Q 043865 41 GFERSYCPNRNCMAL-VVNEGE--INYGTLKKARCPNCKQ 77 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~-~~~~~~--~~~~~~~~~~C~~C~~ 77 (203)
...+-.||+-.|++. +.+-+. .......++.||.|+-
T Consensus 117 ~g~FG~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~D 156 (251)
T PTZ00396 117 QGKFGHCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQE 156 (251)
T ss_pred CCCCCCCCCccCCCCcccccccCCCcCcCceeEeCCCchh
Confidence 456788999999863 333222 1123355566665443
No 236
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=32.07 E-value=1e+02 Score=29.60 Aligned_cols=60 Identities=17% Similarity=0.278 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHHHHhh--c---cC---CCceeCCC-------CCCCceeeecCccccCCCCceeCCCcccc-----ccc
Q 043865 22 IPSNLFSKWCDVLCEDY--V---LG---FERSYCPN-------RNCMALVVNEGEINYGTLKKARCPNCKQW-----FCF 81 (203)
Q Consensus 22 l~~e~~~~y~~~~~~~~--i---~~---~~~~~Cp~-------~~C~~~~~~~~~~~~~~~~~~~C~~C~~~-----~C~ 81 (203)
+|+.++++..+.+.+.. + .. .....|.. |+|+.++..... .....|+.|++. .|-
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~~lt~H~~-----~~~L~CH~Cg~~~~~p~~Cp 479 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDSPLTLHKA-----TGQLRCHYCGYQEPIPQSCP 479 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCccceeecccCCCcccCCCCCcceEEecC-----CCeeEeCCCCCCCCCCCCCC
Confidence 78888888877776652 1 11 11234442 246666665554 577888888876 477
Q ss_pred cCCcC
Q 043865 82 QCKVA 86 (203)
Q Consensus 82 ~C~~~ 86 (203)
.|...
T Consensus 480 ~Cgs~ 484 (730)
T COG1198 480 ECGSE 484 (730)
T ss_pred CCCCC
Confidence 77765
No 237
>PLN00063 photosystem II core complex proteins psbY; Provisional
Probab=31.82 E-value=48 Score=25.97 Aligned_cols=20 Identities=35% Similarity=0.579 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 043865 176 GLILIFTVLGVLGGVIYGIY 195 (203)
Q Consensus 176 ~~~~~f~~l~~~~~~~~~~~ 195 (203)
+.+|+|.+.++||-|+|.|.
T Consensus 162 g~lll~v~~PaigWVlyNIL 181 (194)
T PLN00063 162 GLLLLIVVAPAILWVLYNIL 181 (194)
T ss_pred chhhHHHHHHHHHHHHHHHh
Confidence 35677889999999999885
No 238
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.77 E-value=10 Score=31.44 Aligned_cols=30 Identities=27% Similarity=0.417 Sum_probs=22.4
Q ss_pred CCCCCCceeEecCCcceeEe-ccccccccccccc-CcC
Q 043865 118 RRPACGSCVERKEGCRVMYC-RCKTSFCYECGGN-LKS 153 (203)
Q Consensus 118 ~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~-~~~ 153 (203)
+|+-|-...+ .-.| .||+-|||.|.-. |..
T Consensus 217 kC~lC~e~~~------~ps~t~CgHlFC~~Cl~~~~t~ 248 (271)
T COG5574 217 KCFLCLEEPE------VPSCTPCGHLFCLSCLLISWTK 248 (271)
T ss_pred ceeeeecccC------CcccccccchhhHHHHHHHHHh
Confidence 4777766664 4567 6999999999877 764
No 239
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=31.46 E-value=57 Score=16.90 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=16.0
Q ss_pred CCCCCceeEecCCcceeEe-cccc
Q 043865 119 RPACGSCVERKEGCRVMYC-RCKT 141 (203)
Q Consensus 119 CP~C~~~iek~~GCnhm~C-~C~~ 141 (203)
|-+|+++..--.|=.++.| .|++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 4567777777777777777 5654
No 240
>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=30.68 E-value=46 Score=18.72 Aligned_cols=24 Identities=38% Similarity=0.805 Sum_probs=15.2
Q ss_pred CCCCCCCceeEec-CCcceeEe-ccccc
Q 043865 117 ARRPACGSCVERK-EGCRVMYC-RCKTS 142 (203)
Q Consensus 117 k~CP~C~~~iek~-~GCnhm~C-~C~~~ 142 (203)
-+|+.|+...... +| ..+| +||++
T Consensus 9 ~~C~~C~~~~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCC--EEEhhhCceE
Confidence 3588888874332 44 6667 67664
No 241
>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=30.64 E-value=90 Score=23.26 Aligned_cols=53 Identities=19% Similarity=0.231 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhhcc---CCCceeCCCCCCCceeeecCc------cc----cCCCCceeCCCccccc
Q 043865 25 NLFSKWCDVLCEDYVL---GFERSYCPNRNCMALVVNEGE------IN----YGTLKKARCPNCKQWF 79 (203)
Q Consensus 25 e~~~~y~~~~~~~~i~---~~~~~~Cp~~~C~~~~~~~~~------~~----~~~~~~~~C~~C~~~~ 79 (203)
+..+...+.+....+. .+.+..|| .|++.+..-+. ++ ........||.|++.|
T Consensus 69 ~~~~QL~ev~~~~~l~~~~~~~~sRC~--~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 69 DPEEQLREVLERFGLKLRLDPIFSRCP--KCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CHHHHHHHHHHHcCCccccCCCCCccC--CCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 3444444444444332 44578898 59887754322 11 1224467787777653
No 242
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=30.43 E-value=55 Score=19.89 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=16.6
Q ss_pred CCCCCCCCceeEecC--------CcceeEeccccc
Q 043865 116 GARRPACGSCVERKE--------GCRVMYCRCKTS 142 (203)
Q Consensus 116 ~k~CP~C~~~iek~~--------GCnhm~C~C~~~ 142 (203)
+-.||+|+.-.--++ .=-+=+|+||..
T Consensus 13 Y~~Cp~CGN~~vGngEG~liV~edtfkRtCkCGfn 47 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEGTLIVEEDTFKRTCKCGFN 47 (49)
T ss_pred hccCcccCCcEeecCcceEEEeccceeeeeccccc
Confidence 568999998655442 233446777654
No 243
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.43 E-value=21 Score=32.40 Aligned_cols=34 Identities=26% Similarity=0.612 Sum_probs=24.0
Q ss_pred CccccccccCCcC-CCCCCccccccccccchhHHHHHHHHhccCCCCCCCCceeEe
Q 043865 74 NCKQWFCFQCKVA-WHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVER 128 (203)
Q Consensus 74 ~C~~~~C~~C~~~-~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek 128 (203)
.||+.||+.|-.. |-.+ ...+++.||-|+..|-.
T Consensus 203 ~CGHiFC~~CiLqy~~~s---------------------~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 203 NCGHIFCGPCILQYWNYS---------------------AIKGPCSCPICRSTITL 237 (513)
T ss_pred ccCceeeHHHHHHHHhhh---------------------cccCCccCCchhhhccc
Confidence 4899999988743 2211 24678899999988864
No 244
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.27 E-value=73 Score=22.95 Aligned_cols=48 Identities=17% Similarity=0.332 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHHHHhh-c-c--------CCCceeCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 22 IPSNLFSKWCDVLCEDY-V-L--------GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 22 l~~e~~~~y~~~~~~~~-i-~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
+.++.++-.-..+.+.. + + .+-..+|. +|+..+..+.. ....||.|+.
T Consensus 39 V~pe~L~faf~~~~~~T~~~ega~L~Ie~vp~~~~C~--~Cg~~~~~~~~------~~~~CP~Cgs 96 (117)
T PRK00564 39 MDKSLFVSAFETFREESLVCKDAILDIVDEKVELECK--DCSHVFKPNAL------DYGVCEKCHS 96 (117)
T ss_pred cCHHHHHHHHHHHhcCCcccCCCEEEEEecCCEEEhh--hCCCccccCCc------cCCcCcCCCC
Confidence 34555554444444444 3 2 23457777 58865544322 2235777764
No 245
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.24 E-value=14 Score=23.50 Aligned_cols=26 Identities=23% Similarity=0.611 Sum_probs=15.0
Q ss_pred CCCCCCce----eEecCCcceeEe-cccccc
Q 043865 118 RRPACGSC----VERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 118 ~CP~C~~~----iek~~GCnhm~C-~C~~~F 143 (203)
.||.|+.. ..+..+=.++.| .||++-
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 36666542 234455667777 677764
No 246
>PF09604 Potass_KdpF: F subunit of K+-transporting ATPase (Potass_KdpF); InterPro: IPR011726 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the F subunit (KdpF) of a P-type K+-translocating ATPase (Kdp). KdpF is a very small integral membrane peptide. The kdpABC operon of Escherichia coli codes for the high affinity K+-translocating Kdp complex []. KdpF is found upstream of the KdpA subunit (IPR004623 from INTERPRO). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation. More information about this protein can be found at Protein of the Month: ATP Synthases [].
Probab=30.17 E-value=71 Score=16.54 Aligned_cols=15 Identities=13% Similarity=0.399 Sum_probs=8.3
Q ss_pred HHHHHHHHHHhhhhh
Q 043865 185 GVLGGVIYGIYCVIK 199 (203)
Q Consensus 185 ~~~~~~~~~~~~~~~ 199 (203)
.++++++|-+|.+++
T Consensus 7 v~~~L~~YL~~aLl~ 21 (25)
T PF09604_consen 7 VAVALFVYLFYALLR 21 (25)
T ss_pred HHHHHHHHHHHHHhC
Confidence 344455666666554
No 247
>COG5232 SEC62 Preprotein translocase subunit Sec62 [Intracellular trafficking and secretion]
Probab=29.81 E-value=33 Score=27.62 Aligned_cols=13 Identities=31% Similarity=0.373 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHHH
Q 043865 182 TVLGVLGGVIYGI 194 (203)
Q Consensus 182 ~~l~~~~~~~~~~ 194 (203)
++|.+|++|+||+
T Consensus 158 fvlv~lalVlfpl 170 (259)
T COG5232 158 FVLVTLALVLFPL 170 (259)
T ss_pred HHHHHHHHHHHhc
Confidence 3344444444443
No 248
>TIGR03037 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation.
Probab=29.60 E-value=27 Score=26.80 Aligned_cols=45 Identities=24% Similarity=0.416 Sum_probs=25.2
Q ss_pred ccccccCCcCCCCC-CccccccccccchhHHHHHHHHhccCCCCCCCCc
Q 043865 77 QWFCFQCKVAWHAG-YRCEESGNLRDWNDIAFGKLVERMHGARRPACGS 124 (203)
Q Consensus 77 ~~~C~~C~~~~H~~-~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~ 124 (203)
..+|..|...-|+. ..|.+... .-...+.++..+...++|++|+.
T Consensus 114 ~wyc~~c~~~~~e~~f~~~d~~~---~~~~~~~~f~~~~~~rtC~~Cg~ 159 (159)
T TIGR03037 114 QWFCPQCGHKLHRAEVQLENIVT---DLPPVFEHFYSNEDARTCKNCGH 159 (159)
T ss_pred EEECCCCCCeEEEEEEEecChhh---hhHHHHHHHhCChhhccCCccCC
Confidence 44455565555542 23443221 11245566666778899999984
No 249
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=29.29 E-value=40 Score=25.63 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=11.3
Q ss_pred HHHHHHHHHhhhhhh
Q 043865 186 VLGGVIYGIYCVIKR 200 (203)
Q Consensus 186 ~~~~~~~~~~~~~~~ 200 (203)
.+|+++|.+|-++|.
T Consensus 90 tiGI~~f~lY~l~Ki 104 (152)
T PF15361_consen 90 TIGIVLFILYTLFKI 104 (152)
T ss_pred HHHHHHHHHHHHHHH
Confidence 456778888888874
No 250
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=29.17 E-value=29 Score=21.66 Aligned_cols=14 Identities=21% Similarity=0.420 Sum_probs=7.8
Q ss_pred cCCCceeCCCCCCC
Q 043865 40 LGFERSYCPNRNCM 53 (203)
Q Consensus 40 ~~~~~~~Cp~~~C~ 53 (203)
.......||..+|+
T Consensus 44 ~~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 44 QRNGSKRCPVAGCN 57 (57)
T ss_dssp TTTS-EE-SCCC-S
T ss_pred HhcCCCCCCCCCCC
Confidence 34567889988884
No 251
>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=29.12 E-value=29 Score=18.00 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=15.6
Q ss_pred ccCCcccCCCcCCHHHHhhcCC
Q 043865 2 IECPGVHCDQFLDLFTCKLMIP 23 (203)
Q Consensus 2 I~CP~~~C~~~l~~~~i~~~l~ 23 (203)
+.|| -|.+.++...+...|+
T Consensus 2 v~CP--iC~~~v~~~~in~HLD 21 (26)
T smart00734 2 VQCP--VCFREVPENLINSHLD 21 (26)
T ss_pred CcCC--CCcCcccHHHHHHHHH
Confidence 6789 5998888888877665
No 252
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=29.12 E-value=19 Score=20.50 Aligned_cols=25 Identities=28% Similarity=0.640 Sum_probs=21.2
Q ss_pred CCceeCCCccccccccCCcCCCCCC
Q 043865 67 LKKARCPNCKQWFCFQCKVAWHAGY 91 (203)
Q Consensus 67 ~~~~~C~~C~~~~C~~C~~~~H~~~ 91 (203)
...+.|..|+..+|..|...-|.+.
T Consensus 13 ~~~~~C~~C~~~~C~~C~~~~H~~H 37 (42)
T PF00643_consen 13 PLSLFCEDCNEPLCSECTVSGHKGH 37 (42)
T ss_dssp BEEEEETTTTEEEEHHHHHTSTTTS
T ss_pred ceEEEecCCCCccCccCCCCCCCCC
Confidence 3678999999999999998878763
No 253
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=28.90 E-value=84 Score=25.03 Aligned_cols=41 Identities=22% Similarity=0.434 Sum_probs=27.1
Q ss_pred CCCceeCCCCCCCcee-eecC--ccccCCCCceeCCCccccccc
Q 043865 41 GFERSYCPNRNCMALV-VNEG--EINYGTLKKARCPNCKQWFCF 81 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~~-~~~~--~~~~~~~~~~~C~~C~~~~C~ 81 (203)
..++-.||+-.|.+.- .+-+ +++.....+..||+|.-.+=-
T Consensus 103 ~~dFG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~dvY~P 146 (216)
T KOG3092|consen 103 NGDFGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCEDVYIP 146 (216)
T ss_pred cCCCCcCCcccccCCccccccccCCCCcceEEEeCCCccccccc
Confidence 4678889999987633 2222 234556788899988766543
No 254
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=28.90 E-value=37 Score=18.61 Aligned_cols=25 Identities=20% Similarity=0.530 Sum_probs=20.1
Q ss_pred CCceeCCCccccccccCCcCCCCCC
Q 043865 67 LKKARCPNCKQWFCFQCKVAWHAGY 91 (203)
Q Consensus 67 ~~~~~C~~C~~~~C~~C~~~~H~~~ 91 (203)
...+.|..|+...|..|....|.+.
T Consensus 10 ~~~~fC~~~~~~iC~~C~~~~H~~H 34 (39)
T cd00021 10 PLSLFCETDRALLCVDCDLSVHSGH 34 (39)
T ss_pred ceEEEeCccChhhhhhcChhhcCCC
Confidence 4578899999999999987667653
No 255
>TIGR02115 potass_kdpF K+-transporting ATPase, KdpF subunit. This model describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (TIGR00680). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation.
Probab=28.69 E-value=74 Score=16.65 Aligned_cols=15 Identities=27% Similarity=0.529 Sum_probs=8.1
Q ss_pred HHHHHHHHHHhhhhh
Q 043865 185 GVLGGVIYGIYCVIK 199 (203)
Q Consensus 185 ~~~~~~~~~~~~~~~ 199 (203)
..+++++|-+|.+++
T Consensus 6 l~~~L~~YL~~aLl~ 20 (26)
T TIGR02115 6 LAVGLFIYLFYALLR 20 (26)
T ss_pred HHHHHHHHHHHHHhC
Confidence 344455666665554
No 256
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=28.67 E-value=42 Score=26.23 Aligned_cols=31 Identities=23% Similarity=0.462 Sum_probs=19.2
Q ss_pred CCCceeCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 41 GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 41 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
...+..|| .|...+..+.. ....+.||.||.
T Consensus 110 ~~~~y~C~--~~~~r~sfdeA----~~~~F~Cp~Cg~ 140 (176)
T COG1675 110 ENNYYVCP--NCHVKYSFDEA----MELGFTCPKCGE 140 (176)
T ss_pred cCCceeCC--CCCCcccHHHH----HHhCCCCCCCCc
Confidence 66788895 46655554433 134488887665
No 257
>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=28.46 E-value=28 Score=16.76 Aligned_cols=9 Identities=44% Similarity=1.279 Sum_probs=4.7
Q ss_pred eCCCccccc
Q 043865 71 RCPNCKQWF 79 (203)
Q Consensus 71 ~C~~C~~~~ 79 (203)
.|+.|++.|
T Consensus 2 ~C~~C~~~f 10 (23)
T PF00096_consen 2 KCPICGKSF 10 (23)
T ss_dssp EETTTTEEE
T ss_pred CCCCCCCcc
Confidence 455555543
No 258
>PF11346 DUF3149: Protein of unknown function (DUF3149); InterPro: IPR021494 This bacterial family of proteins has no known function.
Probab=28.41 E-value=1.3e+02 Score=17.63 Aligned_cols=26 Identities=19% Similarity=0.423 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhc
Q 043865 176 GLILIFTVLGVLGGVIYGIYCVIKRV 201 (203)
Q Consensus 176 ~~~~~f~~l~~~~~~~~~~~~~~~~~ 201 (203)
++.-+...+++||...|-..++++++
T Consensus 12 GL~Sl~vI~~~igm~~~~~~~F~~k~ 37 (42)
T PF11346_consen 12 GLMSLIVIVFTIGMGVFFIRYFIRKM 37 (42)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444445556666666666666553
No 259
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=28.39 E-value=34 Score=21.44 Aligned_cols=23 Identities=22% Similarity=0.323 Sum_probs=15.7
Q ss_pred ccCCCCCCCCceeEecCCcceeEe-cccc
Q 043865 114 MHGARRPACGSCVERKEGCRVMYC-RCKT 141 (203)
Q Consensus 114 ~~~k~CP~C~~~iek~~GCnhm~C-~C~~ 141 (203)
.....||+|+.+... |-.| .||+
T Consensus 25 ~~l~~C~~CG~~~~~-----H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPKLP-----HRVCPSCGY 48 (57)
T ss_pred CcceECCCCCCccCC-----eEECCCCCc
Confidence 455679999998863 5555 4553
No 260
>CHL00020 psbN photosystem II protein N
Probab=28.31 E-value=38 Score=20.02 Aligned_cols=19 Identities=21% Similarity=0.254 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHhhhh
Q 043865 180 IFTVLGVLGGVIYGIYCVI 198 (203)
Q Consensus 180 ~f~~l~~~~~~~~~~~~~~ 198 (203)
+|+...++++.-|++|..+
T Consensus 9 i~i~~ll~~~Tgy~iYtaF 27 (43)
T CHL00020 9 IFISGLLVSFTGYALYTAF 27 (43)
T ss_pred HHHHHHHHHhhheeeeecc
Confidence 4444455555567776543
No 261
>PF13153 DUF3985: Protein of unknown function (DUF3985)
Probab=28.27 E-value=1e+02 Score=17.80 Aligned_cols=11 Identities=45% Similarity=0.609 Sum_probs=5.0
Q ss_pred HHHHHHHHHHH
Q 043865 171 CAIISGLILIF 181 (203)
Q Consensus 171 ~~~~~~~~~~f 181 (203)
+++|.+.+|+|
T Consensus 4 la~illvlliy 14 (44)
T PF13153_consen 4 LAIILLVLLIY 14 (44)
T ss_pred HHHHHHHHHHH
Confidence 44554444443
No 262
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=28.20 E-value=37 Score=35.72 Aligned_cols=27 Identities=30% Similarity=0.641 Sum_probs=23.1
Q ss_pred CCCCCCCce------eEecCCcceeEe-cccccccc
Q 043865 117 ARRPACGSC------VERKEGCRVMYC-RCKTSFCY 145 (203)
Q Consensus 117 k~CP~C~~~------iek~~GCnhm~C-~C~~~FC~ 145 (203)
..||.|+.. ++..+||. +| .||+.=|-
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~--~c~~cg~s~c~ 1738 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCA--TCPVCGWSKCV 1738 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCce--eCCCCCCcccc
Confidence 459999999 78889997 99 79998774
No 263
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=27.74 E-value=30 Score=33.71 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=19.0
Q ss_pred CCCCCCCc-eeEecCCcceeEe-ccccc
Q 043865 117 ARRPACGS-CVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 117 k~CP~C~~-~iek~~GCnhm~C-~C~~~ 142 (203)
-.||-|+. .||..+||| || .|+.+
T Consensus 828 ~~cp~c~~~~~~~~~~c~--~c~~c~~~ 853 (858)
T PRK08115 828 NTCPVCREGTVEEIGGCN--TCTNCGAQ 853 (858)
T ss_pred CCCCccCCCceeecCCCc--cccchhhh
Confidence 48999987 678889999 67 57654
No 264
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=27.60 E-value=29 Score=27.08 Aligned_cols=51 Identities=18% Similarity=0.279 Sum_probs=29.3
Q ss_pred cccccccCCcCCCCC-CccccccccccchhHHHHHHHHhccCCCCCCCCceeEec
Q 043865 76 KQWFCFQCKVAWHAG-YRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERK 129 (203)
Q Consensus 76 ~~~~C~~C~~~~H~~-~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~ 129 (203)
-..||..|...-|+. ..|.+... .-...+.++..+...++|++|+......
T Consensus 119 ~~wyc~~c~~~~~e~~f~~~d~~~---~~~~~~~~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 119 FQWYCDECNHKVHEVEVQLTDIET---DLPPVFAAFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred eEEECCCCCCeEEEEEEEecChhh---hhHHHHHHHhcCHhhccCCcCCcccCcc
Confidence 344555566555542 23443221 1124566666677889999999876543
No 265
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=27.23 E-value=43 Score=19.11 Aligned_cols=20 Identities=25% Similarity=0.740 Sum_probs=13.5
Q ss_pred CCCCCCCceeEec---CCcceeEe
Q 043865 117 ARRPACGSCVERK---EGCRVMYC 137 (203)
Q Consensus 117 k~CP~C~~~iek~---~GCnhm~C 137 (203)
+.||.|+..+... .| ..+.|
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-~F~~C 24 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-KFLGC 24 (39)
T ss_pred cCCCCCCceeEEEECCCC-CEEEC
Confidence 5799999765543 45 66666
No 266
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=27.21 E-value=42 Score=19.17 Aligned_cols=18 Identities=22% Similarity=0.741 Sum_probs=15.3
Q ss_pred ceeCCCccccccccCCcC
Q 043865 69 KARCPNCKQWFCFQCKVA 86 (203)
Q Consensus 69 ~~~C~~C~~~~C~~C~~~ 86 (203)
.+.|..|+..||.+-+.+
T Consensus 12 ~f~C~~C~~~FC~~HR~~ 29 (39)
T smart00154 12 GFKCRHCGNLFCGEHRLP 29 (39)
T ss_pred CeECCccCCccccccCCc
Confidence 588999999999887754
No 267
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=27.08 E-value=2.1e+02 Score=21.39 Aligned_cols=39 Identities=10% Similarity=0.161 Sum_probs=21.9
Q ss_pred hccCCCCCCCCceeEecCCcceeEecccccccccccccCcC-CCCCCCCcC
Q 043865 113 RMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKS-ASGCLCKEK 162 (203)
Q Consensus 113 ~~~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~-~~~C~~~~~ 162 (203)
....+-|+.|+..- -. +.+.|..|++-... .+.|+...+
T Consensus 45 ~~~~~~C~~C~~~k--p~---------Rs~HC~~C~~CV~~~DHHC~w~~~ 84 (174)
T PF01529_consen 45 NGELKYCSTCKIIK--PP---------RSHHCRVCNRCVLRFDHHCPWLGN 84 (174)
T ss_pred CCCCEECcccCCcC--CC---------cceeccccccccccccccchhhcc
Confidence 34567899987653 11 45566666655443 234665554
No 268
>PF06084 Cytomega_TRL10: Cytomegalovirus TRL10 protein; InterPro: IPR009284 This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulphide-linked complex [].
Probab=27.03 E-value=74 Score=23.03 Aligned_cols=12 Identities=17% Similarity=0.617 Sum_probs=8.5
Q ss_pred CCcceeEecccc
Q 043865 130 EGCRVMYCRCKT 141 (203)
Q Consensus 130 ~GCnhm~C~C~~ 141 (203)
+|=.|++|+|..
T Consensus 15 ~~~t~l~ckc~~ 26 (150)
T PF06084_consen 15 SENTHLTCKCSP 26 (150)
T ss_pred cCCeeEEEecCC
Confidence 556688888863
No 269
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=26.90 E-value=1e+02 Score=22.54 Aligned_cols=29 Identities=24% Similarity=0.435 Sum_probs=22.6
Q ss_pred ccCCCCCCCCc---eeEecCCcceeEe-ccccc
Q 043865 114 MHGARRPACGS---CVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 114 ~~~k~CP~C~~---~iek~~GCnhm~C-~C~~~ 142 (203)
...-.||.|+. .+.+.++=-.+.| .||..
T Consensus 91 ~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 91 KEYVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp CHHSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HHEEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 34568999987 4667788899999 69964
No 270
>PF06143 Baculo_11_kDa: Baculovirus 11 kDa family; InterPro: IPR009313 This is a family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.
Probab=26.21 E-value=1.4e+02 Score=20.39 Aligned_cols=18 Identities=22% Similarity=0.276 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHHHhhhh
Q 043865 181 FTVLGVLGGVIYGIYCVI 198 (203)
Q Consensus 181 f~~l~~~~~~~~~~~~~~ 198 (203)
++++.++.++++-+|.+.
T Consensus 43 ~lVfVii~lFi~ll~~i~ 60 (84)
T PF06143_consen 43 FLVFVIIVLFILLLYNIN 60 (84)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344444444444444433
No 271
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=26.19 E-value=54 Score=23.54 Aligned_cols=35 Identities=23% Similarity=0.424 Sum_probs=25.8
Q ss_pred cCCCCCCCCceeEecCCcceeEe-ccccccccccccc
Q 043865 115 HGARRPACGSCVERKEGCRVMYC-RCKTSFCYECGGN 150 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~ 150 (203)
+.+.|..|+...-...+.. ..| .|++.+|-.|+..
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccccCccCCc
Confidence 4578999998766555555 788 6999999999887
No 272
>COG5487 Small integral membrane protein [Function unknown]
Probab=26.04 E-value=1.1e+02 Score=18.73 Aligned_cols=13 Identities=31% Similarity=0.360 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHH
Q 043865 176 GLILIFTVLGVLG 188 (203)
Q Consensus 176 ~~~~~f~~l~~~~ 188 (203)
..+|+|+++.++.
T Consensus 31 AkIlF~i~~vlf~ 43 (54)
T COG5487 31 AKILFFIFLVLFL 43 (54)
T ss_pred HHHHHHHHHHHHH
Confidence 4566666655543
No 273
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=25.79 E-value=1.3e+02 Score=19.86 Aligned_cols=38 Identities=11% Similarity=0.076 Sum_probs=22.8
Q ss_pred hcCCHHHHHHHHHHHHHhhcc--CCCceeCCCCCCCceee
Q 043865 20 LMIPSNLFSKWCDVLCEDYVL--GFERSYCPNRNCMALVV 57 (203)
Q Consensus 20 ~~l~~e~~~~y~~~~~~~~i~--~~~~~~Cp~~~C~~~~~ 57 (203)
.-+++|-.+--++++.-+.-. ..+.+.||..+|.+...
T Consensus 11 ~r~s~ey~~Gv~~Fi~~A~~~~~~~~~i~CPC~~C~N~~~ 50 (77)
T PF13963_consen 11 DRFSPEYIEGVEEFIDFAFSNPSNDNMIRCPCRKCKNEKR 50 (77)
T ss_pred CCCCHHHHHHHHHHHHHHHhcccCCCceECCchhhccCcc
Confidence 345666555555554444322 33489999999987665
No 274
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=25.70 E-value=73 Score=19.85 Aligned_cols=31 Identities=29% Similarity=0.426 Sum_probs=16.7
Q ss_pred CceeCCCCCCCcee----eecCccccCCCCceeCCCcccc
Q 043865 43 ERSYCPNRNCMALV----VNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 43 ~~~~Cp~~~C~~~~----~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
.++.||. |++-- ..+.. -...-..||.|+++
T Consensus 3 ~Wi~CP~--CgnKTR~kir~DT~---LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 3 EWILCPI--CGNKTRLKIREDTV---LKNFPLYCPKCKQE 37 (55)
T ss_pred eEEECCC--CCCccceeeecCce---eccccccCCCCCce
Confidence 4678884 77532 12222 12555677776654
No 275
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=25.69 E-value=58 Score=23.23 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=17.4
Q ss_pred CCCCCCCceeEecCCcceeEe-cccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYC-RCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C-~C~~~F 143 (203)
..||+|+.-..=.+|= +|.| -|.++|
T Consensus 4 p~cp~c~sEytYed~~-~~~cpec~~ew 30 (112)
T COG2824 4 PPCPKCNSEYTYEDGG-QLICPECAHEW 30 (112)
T ss_pred CCCCccCCceEEecCc-eEeCchhcccc
Confidence 5799997655544443 8888 577665
No 276
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=25.65 E-value=23 Score=34.26 Aligned_cols=38 Identities=26% Similarity=0.621 Sum_probs=0.0
Q ss_pred cCCCCCCCCceeEecCCcceeEe-ccccc-----ccccccccCcCCCCCCC
Q 043865 115 HGARRPACGSCVERKEGCRVMYC-RCKTS-----FCYECGGNLKSASGCLC 159 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~~~~~~~C~~ 159 (203)
..++||+|+.... .-+| .||.+ +|..|+.+.... .|++
T Consensus 654 ~~r~Cp~Cg~~t~------~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-~C~~ 697 (900)
T PF03833_consen 654 GRRRCPKCGKETF------YNRCPECGSHTEPVYVCPDCGIEVEED-ECPK 697 (900)
T ss_dssp ---------------------------------------------------
T ss_pred ecccCcccCCcch------hhcCcccCCccccceeccccccccCcc-cccc
Confidence 3489999998764 5678 68866 899998888764 2443
No 277
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=25.32 E-value=55 Score=24.19 Aligned_cols=26 Identities=23% Similarity=0.538 Sum_probs=16.2
Q ss_pred CCCCC--CCCceeEecCCcceeEe-ccccc
Q 043865 116 GARRP--ACGSCVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 116 ~k~CP--~C~~~iek~~GCnhm~C-~C~~~ 142 (203)
...|| .|+..+... |=+..+| +|+..
T Consensus 18 Y~aC~~~~C~kKv~~~-~~~~y~C~~C~~~ 46 (146)
T PF08646_consen 18 YPACPNEKCNKKVTEN-GDGSYRCEKCNKT 46 (146)
T ss_dssp EEE-TSTTTS-B-EEE-TTTEEEETTTTEE
T ss_pred ECCCCCccCCCEeecC-CCcEEECCCCCCc
Confidence 36799 999988877 3356777 67644
No 278
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=25.14 E-value=69 Score=22.90 Aligned_cols=33 Identities=15% Similarity=0.454 Sum_probs=19.1
Q ss_pred CceeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865 43 ERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW 78 (203)
Q Consensus 43 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~ 78 (203)
++++|+ .|++.+.+..+ ..+..-...|..|.+.
T Consensus 3 ~~rfC~--eCNNmLYPkED-ked~~L~laCrnCd~v 35 (113)
T KOG2691|consen 3 GIRFCR--ECNNMLYPKED-KEDRILLLACRNCDYV 35 (113)
T ss_pred ccchhh--hhhcccccccc-ccccEEEEEecCCcce
Confidence 356777 68888766443 1123445566666554
No 279
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.11 E-value=38 Score=21.84 Aligned_cols=17 Identities=29% Similarity=0.366 Sum_probs=13.2
Q ss_pred cCCCCCCCCceeEecCC
Q 043865 115 HGARRPACGSCVERKEG 131 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~G 131 (203)
.+..||.|+.+++..+-
T Consensus 6 ~~v~CP~Cgkpv~w~~~ 22 (65)
T COG3024 6 ITVPCPTCGKPVVWGEE 22 (65)
T ss_pred ccccCCCCCCccccccc
Confidence 45789999999987543
No 280
>PHA03164 hypothetical protein; Provisional
Probab=24.94 E-value=86 Score=20.95 Aligned_cols=19 Identities=16% Similarity=0.259 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHhhh
Q 043865 179 LIFTVLGVLGGVIYGIYCV 197 (203)
Q Consensus 179 ~~f~~l~~~~~~~~~~~~~ 197 (203)
|--+.+++|+.++|.+|++
T Consensus 63 LtgLaIamILfiifvlyvF 81 (88)
T PHA03164 63 LTGLAIAMILFIIFVLYVF 81 (88)
T ss_pred HHHHHHHHHHHHHHHHHhe
Confidence 3333444444455555543
No 281
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=24.78 E-value=1.3e+02 Score=21.79 Aligned_cols=47 Identities=21% Similarity=0.407 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHHhhcc---------CCCceeCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 22 IPSNLFSKWCDVLCEDYVL---------GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 22 l~~e~~~~y~~~~~~~~i~---------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
+.++.++---+...+.++. .+-..||. +|+..+..+.. ...||.|+.
T Consensus 39 v~~~~l~FaFev~~egT~aega~l~Ie~~p~~~~C~--~C~~~~~~e~~-------~~~CP~C~s 94 (115)
T COG0375 39 VEPEALRFAFEVVAEGTIAEGAELHIEEEPAECWCL--DCGQEVELEEL-------DYRCPKCGS 94 (115)
T ss_pred cCHHHHHHHHHHHhccCcccCCEEEEEEeccEEEec--cCCCeecchhh-------eeECCCCCC
Confidence 4556555444444444332 34457887 68877776554 344888764
No 282
>PF04639 Baculo_E56: Baculoviral E56 protein, specific to ODV envelope; InterPro: IPR006733 This family represents the E56 protein, which is localized to the occlusion derived virus (ODV) envelope, but not to the budded virus (BV) envelope []. Signals necessary for transport and/or retention into this structure are believed to be found within the C-terminal portion of ODV-E56.; GO: 0019031 viral envelope
Probab=24.45 E-value=56 Score=27.56 Aligned_cols=18 Identities=22% Similarity=0.412 Sum_probs=10.6
Q ss_pred HHHHHHHHHHhhhhhhcc
Q 043865 185 GVLGGVIYGIYCVIKRVL 202 (203)
Q Consensus 185 ~~~~~~~~~~~~~~~~~~ 202 (203)
+.+++++|..|++||++.
T Consensus 285 G~vl~i~~Ig~~ifK~~~ 302 (305)
T PF04639_consen 285 GGVLLIVFIGYFIFKRLM 302 (305)
T ss_pred HHHHHHHHhhheeeEeec
Confidence 333444666777777653
No 283
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=24.44 E-value=17 Score=30.95 Aligned_cols=17 Identities=29% Similarity=0.405 Sum_probs=13.6
Q ss_pred CCCCCCCCceeEecCCc
Q 043865 116 GARRPACGSCVERKEGC 132 (203)
Q Consensus 116 ~k~CP~C~~~iek~~GC 132 (203)
.|-||.|.-.|+|.+-|
T Consensus 123 dK~Cp~C~d~VqrIeq~ 139 (389)
T KOG2932|consen 123 DKICPLCDDRVQRIEQI 139 (389)
T ss_pred cccCcCcccHHHHHHHh
Confidence 36788888888888766
No 284
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=24.41 E-value=25 Score=26.05 Aligned_cols=23 Identities=30% Similarity=0.674 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHhhhhhhcc
Q 043865 180 IFTVLGVLGGVIYGIYCVIKRVL 202 (203)
Q Consensus 180 ~f~~l~~~~~~~~~~~~~~~~~~ 202 (203)
+|+.+.++|++-|++|-+.|+++
T Consensus 110 ~~~~a~~~~Gl~~~~y~~~k~~v 132 (136)
T PF04695_consen 110 VFITAYAFGGLGYGLYGLSKKYV 132 (136)
T ss_dssp -----------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Confidence 46667788889999999998875
No 285
>PF14018 DUF4234: Domain of unknown function (DUF4234)
Probab=24.34 E-value=1.1e+02 Score=19.75 Aligned_cols=19 Identities=32% Similarity=0.658 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHhhhhh
Q 043865 181 FTVLGVLGGVIYGIYCVIK 199 (203)
Q Consensus 181 f~~l~~~~~~~~~~~~~~~ 199 (203)
+++|+++-+=||++|-+-|
T Consensus 6 ~ilLsiiT~GIY~l~W~y~ 24 (75)
T PF14018_consen 6 VILLSIITCGIYGLYWLYK 24 (75)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444555554433
No 286
>TIGR01195 oadG_fam sodium pump decarboxylases, gamma subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins.
Probab=24.16 E-value=1.8e+02 Score=19.55 Aligned_cols=26 Identities=19% Similarity=0.085 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhh
Q 043865 175 SGLILIFTVLGVLGGVIYGIYCVIKR 200 (203)
Q Consensus 175 ~~~~~~f~~l~~~~~~~~~~~~~~~~ 200 (203)
+..+-|-+++..|++++|.+.++-|.
T Consensus 10 l~v~GM~~VF~fL~lLi~~i~~~~~~ 35 (82)
T TIGR01195 10 LTVLGMGIVFLFLSLLIYAVRGMGKV 35 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566667777777777776554
No 287
>smart00336 BBOX B-Box-type zinc finger.
Probab=24.14 E-value=69 Score=17.75 Aligned_cols=24 Identities=29% Similarity=0.624 Sum_probs=19.1
Q ss_pred CCceeCCCccccccccCCcCCCCC
Q 043865 67 LKKARCPNCKQWFCFQCKVAWHAG 90 (203)
Q Consensus 67 ~~~~~C~~C~~~~C~~C~~~~H~~ 90 (203)
...+.|..|....|..|...-|.+
T Consensus 13 ~~~~~C~~c~~~iC~~C~~~~H~~ 36 (42)
T smart00336 13 PAEFFCEECGALLCRTCDEAEHRG 36 (42)
T ss_pred ceEEECCCCCcccccccChhhcCC
Confidence 456789999999999998766654
No 288
>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=24.06 E-value=43 Score=18.55 Aligned_cols=13 Identities=31% Similarity=0.598 Sum_probs=9.0
Q ss_pred CCCCCCCceeEec
Q 043865 117 ARRPACGSCVERK 129 (203)
Q Consensus 117 k~CP~C~~~iek~ 129 (203)
-.||+|+..|.-+
T Consensus 5 ~~C~nC~R~v~a~ 17 (33)
T PF08209_consen 5 VECPNCGRPVAAS 17 (33)
T ss_dssp EE-TTTSSEEEGG
T ss_pred EECCCCcCCcchh
Confidence 4699999988643
No 289
>PHA01399 membrane protein P6
Probab=24.03 E-value=97 Score=24.55 Aligned_cols=25 Identities=16% Similarity=0.404 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhh
Q 043865 176 GLILIFTVLGVLGGVIYGIYCVIKR 200 (203)
Q Consensus 176 ~~~~~f~~l~~~~~~~~~~~~~~~~ 200 (203)
+.||+.+++.+.+-++||.+.++.+
T Consensus 59 g~il~~il~~~~awf~fpa~IAIIK 83 (242)
T PHA01399 59 GIILIIILIIIAAWFFFPAFAAFLQ 83 (242)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555666678888776643
No 290
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=24.02 E-value=45 Score=27.55 Aligned_cols=37 Identities=27% Similarity=0.723 Sum_probs=22.8
Q ss_pred CCCCCCCCcee-----EecCCcceeEe-cccccc-----------cccccccCc
Q 043865 116 GARRPACGSCV-----ERKEGCRVMYC-RCKTSF-----------CYECGGNLK 152 (203)
Q Consensus 116 ~k~CP~C~~~i-----ek~~GCnhm~C-~C~~~F-----------C~~C~~~~~ 152 (203)
+.+|-+|+... .|..|=-...| .|++.| ||.|+.+..
T Consensus 132 VSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v~ 185 (278)
T PF15135_consen 132 VSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNPVY 185 (278)
T ss_pred cccccccccccCCCccccccceeeeecccccccchhhhhcCCCCCccCCCCccC
Confidence 34566665543 34466666667 576666 888877754
No 291
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=23.99 E-value=75 Score=27.27 Aligned_cols=16 Identities=25% Similarity=0.492 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHHHhh
Q 043865 181 FTVLGVLGGVIYGIYC 196 (203)
Q Consensus 181 f~~l~~~~~~~~~~~~ 196 (203)
.++|.+|+.+||.+++
T Consensus 162 ii~l~vla~ivY~~~~ 177 (318)
T PF06682_consen 162 IIFLLVLAFIVYSLFL 177 (318)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3444555555555544
No 292
>PF15128 T_cell_tran_alt: T-cell leukemia translocation-altered
Probab=23.96 E-value=1.7e+02 Score=20.04 Aligned_cols=19 Identities=32% Similarity=0.354 Sum_probs=10.6
Q ss_pred hHHHHHHHHHHHHHHHHHHH
Q 043865 170 YCAIISGLILIFTVLGVLGG 189 (203)
Q Consensus 170 ~~~~~~~~~~~f~~l~~~~~ 189 (203)
+.++| .++|..++|++|++
T Consensus 24 rv~if-kllL~WlvlsLl~I 42 (92)
T PF15128_consen 24 RVQIF-KLLLGWLVLSLLAI 42 (92)
T ss_pred HHHHH-HHHHHHHHHHHHHH
Confidence 34444 33445777777764
No 293
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=23.93 E-value=51 Score=24.95 Aligned_cols=26 Identities=23% Similarity=0.505 Sum_probs=17.9
Q ss_pred CCCCCCCCceeEecCCcceeEe-ccccc
Q 043865 116 GARRPACGSCVERKEGCRVMYC-RCKTS 142 (203)
Q Consensus 116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~ 142 (203)
+..||.|+..+...+. ....| +|+..
T Consensus 34 Y~aC~~C~kkv~~~~~-~~~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKKVVEEGN-GTYRCEKCNKS 60 (166)
T ss_pred EccccccCcccEeCCC-CcEECCCCCCc
Confidence 4789999999987654 44555 45543
No 294
>PF13150 DUF3989: Protein of unknown function (DUF3989)
Probab=23.74 E-value=1.7e+02 Score=19.90 Aligned_cols=16 Identities=13% Similarity=0.351 Sum_probs=7.9
Q ss_pred hHHHHHHHHHHHHHHH
Q 043865 170 YCAIISGLILIFTVLG 185 (203)
Q Consensus 170 ~~~~~~~~~~~f~~l~ 185 (203)
+..+++.++++|.+|+
T Consensus 27 R~~vvl~ml~~fa~l~ 42 (85)
T PF13150_consen 27 RLRVVLVMLVLFAALC 42 (85)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4455544455555543
No 295
>KOG1307 consensus K+-dependent Ca2+/Na+ exchanger NCKX1 and related proteins [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=23.64 E-value=97 Score=28.21 Aligned_cols=28 Identities=25% Similarity=0.389 Sum_probs=17.6
Q ss_pred HHHHHHHHHHH--------HHHHHHHHHHhhhhhhc
Q 043865 174 ISGLILIFTVL--------GVLGGVIYGIYCVIKRV 201 (203)
Q Consensus 174 ~~~~~~~f~~l--------~~~~~~~~~~~~~~~~~ 201 (203)
+++++|+++++ +++.+.+|..|+++-++
T Consensus 169 lsl~~Li~Ff~D~~I~WwEaL~L~~~Yi~Yv~~MKf 204 (588)
T KOG1307|consen 169 LSLIMLIYFFLDELIMWWEALALLLMYISYVVFMKF 204 (588)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHheeeeh
Confidence 34455555544 55566799999887543
No 296
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=23.34 E-value=92 Score=22.45 Aligned_cols=16 Identities=25% Similarity=0.318 Sum_probs=10.6
Q ss_pred HHHHHHHHHHhhhhhh
Q 043865 185 GVLGGVIYGIYCVIKR 200 (203)
Q Consensus 185 ~~~~~~~~~~~~~~~~ 200 (203)
..|++|-|-||+++.+
T Consensus 73 vSLaLVsFvIFLiiQT 88 (128)
T PF15145_consen 73 VSLALVSFVIFLIIQT 88 (128)
T ss_pred HHHHHHHHHHHheeec
Confidence 4456677778877754
No 297
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=22.90 E-value=25 Score=29.71 Aligned_cols=29 Identities=24% Similarity=0.571 Sum_probs=22.0
Q ss_pred CCCCCCCceeEecCCcceeEe--cccccccccccccCc
Q 043865 117 ARRPACGSCVERKEGCRVMYC--RCKTSFCYECGGNLK 152 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C--~C~~~FC~~C~~~~~ 152 (203)
-+|--|.-.+ .+-| .||+-||++|-+..-
T Consensus 26 lrC~IC~~~i-------~ip~~TtCgHtFCslCIR~hL 56 (391)
T COG5432 26 LRCRICDCRI-------SIPCETTCGHTFCSLCIRRHL 56 (391)
T ss_pred HHhhhhhhee-------ecceecccccchhHHHHHHHh
Confidence 4677777666 5778 599999999976644
No 298
>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=22.89 E-value=46 Score=15.61 Aligned_cols=8 Identities=38% Similarity=1.098 Sum_probs=3.0
Q ss_pred eCCCcccc
Q 043865 71 RCPNCKQW 78 (203)
Q Consensus 71 ~C~~C~~~ 78 (203)
.|+.|+..
T Consensus 2 ~C~~C~~~ 9 (24)
T PF13894_consen 2 QCPICGKS 9 (24)
T ss_dssp E-SSTS-E
T ss_pred CCcCCCCc
Confidence 45555544
No 299
>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=22.71 E-value=34 Score=21.52 Aligned_cols=14 Identities=36% Similarity=0.655 Sum_probs=6.9
Q ss_pred CCCCCCCceeEecC
Q 043865 117 ARRPACGSCVERKE 130 (203)
Q Consensus 117 k~CP~C~~~iek~~ 130 (203)
.+||.|+..++-..
T Consensus 3 v~CP~C~k~~~~~~ 16 (57)
T PF03884_consen 3 VKCPICGKPVEWSP 16 (57)
T ss_dssp EE-TTT--EEE-SS
T ss_pred ccCCCCCCeecccC
Confidence 46888888887643
No 300
>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=22.61 E-value=91 Score=18.52 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=15.9
Q ss_pred eCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865 46 YCPNRNCMALVVNEGEINYGTLKKARCPNCKQ 77 (203)
Q Consensus 46 ~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~ 77 (203)
.|+ +|+..+......+ ......||.|+.
T Consensus 7 ~C~--~Cg~~fe~~~~~~--~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCT--ACGHRFEVLQKMS--DDPLATCPECGG 34 (52)
T ss_pred EeC--CCCCEeEEEEecC--CCCCCCCCCCCC
Confidence 465 6887554332211 135577888876
No 301
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=22.48 E-value=1.4e+02 Score=20.51 Aligned_cols=13 Identities=15% Similarity=-0.090 Sum_probs=5.6
Q ss_pred HHHHHHHHHHHHH
Q 043865 179 LIFTVLGVLGGVI 191 (203)
Q Consensus 179 ~~f~~l~~~~~~~ 191 (203)
++.+++.++|++.
T Consensus 10 ~~~v~~~i~~y~~ 22 (87)
T PF10883_consen 10 VGAVVALILAYLW 22 (87)
T ss_pred HHHHHHHHHHHHH
Confidence 3344444444443
No 302
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=22.33 E-value=1.2e+02 Score=25.78 Aligned_cols=23 Identities=13% Similarity=0.288 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhh
Q 043865 177 LILIFTVLGVLGGVIYGIYCVIK 199 (203)
Q Consensus 177 ~~~~f~~l~~~~~~~~~~~~~~~ 199 (203)
++-..+++.+|.+|...||++.|
T Consensus 258 I~aSiiaIliIVLIMvIIYLILR 280 (299)
T PF02009_consen 258 IIASIIAILIIVLIMVIIYLILR 280 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456666666667778888765
No 303
>PRK14762 membrane protein; Provisional
Probab=22.25 E-value=1.3e+02 Score=15.53 Aligned_cols=6 Identities=33% Similarity=1.077 Sum_probs=2.7
Q ss_pred HHHHHh
Q 043865 190 VIYGIY 195 (203)
Q Consensus 190 ~~~~~~ 195 (203)
++++.+
T Consensus 18 vvtgvf 23 (27)
T PRK14762 18 VVTGVF 23 (27)
T ss_pred HHHHHH
Confidence 344444
No 304
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=22.23 E-value=22 Score=22.77 Aligned_cols=40 Identities=15% Similarity=0.163 Sum_probs=22.8
Q ss_pred cCCCCCCCCceeEecCCcceeEecccccccccccccCcCC
Q 043865 115 HGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSA 154 (203)
Q Consensus 115 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~~ 154 (203)
...+||+|...-.|----|.-.=.=-.+||-.|..-|+.+
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~G 43 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHG 43 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhc
Confidence 4578999987654433322222223356777777777754
No 305
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=22.22 E-value=32 Score=23.52 Aligned_cols=35 Identities=20% Similarity=0.476 Sum_probs=28.1
Q ss_pred CCCCCCCceeEecCCcceeEecccccccccccccCcCC
Q 043865 117 ARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSA 154 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~~ 154 (203)
..||.|..+ .+.|--+...|++.|=.-|...|...
T Consensus 33 g~Cp~Ck~P---gd~Cplv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 33 GCCPDCKFP---GDDCPLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred cCCCCccCC---CCCCceeeccCccHHHHHHHHHHHcc
Confidence 357888776 46687788899999999999988864
No 306
>PF07234 DUF1426: Protein of unknown function (DUF1426); InterPro: IPR009871 This family consists of several Banana bunchy top virus proteins of around 120 residues in length. Q9IGU4 from SWISSPROT is annotated a movement protein whereas most other family members are hypothetical. The function of this family is unknown.
Probab=21.95 E-value=1.1e+02 Score=21.60 Aligned_cols=14 Identities=14% Similarity=0.574 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHH
Q 043865 174 ISGLILIFTVLGVL 187 (203)
Q Consensus 174 ~~~~~~~f~~l~~~ 187 (203)
|+++-.+||+|.+|
T Consensus 22 FiAItIlYILLalL 35 (117)
T PF07234_consen 22 FIAITILYILLALL 35 (117)
T ss_pred HHHHHHHHHHHHHH
Confidence 33444445554444
No 307
>PRK13454 F0F1 ATP synthase subunit B'; Provisional
Probab=21.90 E-value=1.2e+02 Score=23.46 Aligned_cols=17 Identities=24% Similarity=0.266 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHHHHH
Q 043865 177 LILIFTVLGVLGGVIYG 193 (203)
Q Consensus 177 ~~~~f~~l~~~~~~~~~ 193 (203)
++.+++++.+|..++||
T Consensus 38 lI~F~iL~~ll~k~l~~ 54 (181)
T PRK13454 38 LVTLVAIYFVLTRVALP 54 (181)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33444444555566676
No 308
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=21.88 E-value=1.4e+02 Score=22.01 Aligned_cols=17 Identities=29% Similarity=0.749 Sum_probs=9.7
Q ss_pred ccccCCcCCCCCCcccc
Q 043865 79 FCFQCKVAWHAGYRCEE 95 (203)
Q Consensus 79 ~C~~C~~~~H~~~~C~~ 95 (203)
.|+.|...-|....|.+
T Consensus 54 ~C~~Cg~~GH~~~~Cp~ 70 (148)
T PTZ00368 54 SCYNCGKTGHLSRECPE 70 (148)
T ss_pred ccCCCCCcCcCcccCCC
Confidence 46666665565555543
No 309
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=21.81 E-value=1.8e+02 Score=20.19 Aligned_cols=15 Identities=7% Similarity=0.005 Sum_probs=9.8
Q ss_pred CcCCHHHHhhcCCHH
Q 043865 11 QFLDLFTCKLMIPSN 25 (203)
Q Consensus 11 ~~l~~~~i~~~l~~e 25 (203)
..++..++..+++.+
T Consensus 17 eplt~~ei~~~~~~~ 31 (97)
T COG3357 17 EPLTVAEIFELLNGE 31 (97)
T ss_pred CcchHHHHHHHHcCC
Confidence 456677777777643
No 310
>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=21.60 E-value=1.2e+02 Score=17.09 Aligned_cols=30 Identities=23% Similarity=0.681 Sum_probs=15.6
Q ss_pred ceeCCCCCCCcee--eecCccccCCCCceeCCCcc
Q 043865 44 RSYCPNRNCMALV--VNEGEINYGTLKKARCPNCK 76 (203)
Q Consensus 44 ~~~Cp~~~C~~~~--~~~~~~~~~~~~~~~C~~C~ 76 (203)
.+.||. |+..- ...+. +.++.+...|..|+
T Consensus 5 ~v~CP~--C~s~~~v~k~G~-~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 5 DVHCPR--CQSTEGVKKNGK-SPSGHQRYRCKDCR 36 (36)
T ss_pred eeeCCC--CCCCCcceeCCC-CCCCCEeEecCcCC
Confidence 367884 65433 22222 23446677776653
No 311
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=20.89 E-value=96 Score=25.69 Aligned_cols=13 Identities=31% Similarity=0.815 Sum_probs=6.5
Q ss_pred CCceeCCCcccccc
Q 043865 67 LKKARCPNCKQWFC 80 (203)
Q Consensus 67 ~~~~~C~~C~~~~C 80 (203)
...-+||. +...|
T Consensus 64 ~~~~~Cp~-~t~vC 76 (268)
T PF09451_consen 64 PKEDQCPT-GTRVC 76 (268)
T ss_pred CccccCcC-CCcEE
Confidence 33445654 44555
No 312
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=20.81 E-value=99 Score=20.39 Aligned_cols=36 Identities=28% Similarity=0.552 Sum_probs=27.2
Q ss_pred ccCCCCCCCCceeE--ecCCcceeEe--cccccccccccc
Q 043865 114 MHGARRPACGSCVE--RKEGCRVMYC--RCKTSFCYECGG 149 (203)
Q Consensus 114 ~~~k~CP~C~~~ie--k~~GCnhm~C--~C~~~FC~~C~~ 149 (203)
..-..||.|+..=. ....|.--.| .=+.+||+.|..
T Consensus 32 ~~~~~C~GCr~~~~~~~~~~C~i~~C~~ekgv~~C~eC~e 71 (78)
T PF12675_consen 32 PEKIRCPGCRSGGGKCCCKSCKIRQCAKEKGVDFCGECPE 71 (78)
T ss_pred CCCCcCcCCcCCCCCcCCCCCCcCcHHhhCCCCeeecCCC
Confidence 34478999988763 5567888888 258899999965
No 313
>PF06682 DUF1183: Protein of unknown function (DUF1183); InterPro: IPR009567 This family consists of several eukaryotic proteins of around 360 residues in length. The function of this family is unknown.
Probab=20.75 E-value=89 Score=26.82 Aligned_cols=19 Identities=11% Similarity=0.093 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHhhhhh
Q 043865 181 FTVLGVLGGVIYGIYCVIK 199 (203)
Q Consensus 181 f~~l~~~~~~~~~~~~~~~ 199 (203)
++++++|++++|.||-++.
T Consensus 159 lf~ii~l~vla~ivY~~~~ 177 (318)
T PF06682_consen 159 LFWIIFLLVLAFIVYSLFL 177 (318)
T ss_pred hhhHHHHHHHHHHHHHHHh
Confidence 4555555555666665554
No 314
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=20.71 E-value=41 Score=29.20 Aligned_cols=9 Identities=33% Similarity=0.648 Sum_probs=6.2
Q ss_pred CCCCCCCCc
Q 043865 116 GARRPACGS 124 (203)
Q Consensus 116 ~k~CP~C~~ 124 (203)
.|+||.|+.
T Consensus 67 RKRCP~CRF 75 (475)
T KOG4218|consen 67 RKRCPSCRF 75 (475)
T ss_pred hccCCchhH
Confidence 478887754
No 315
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=20.68 E-value=63 Score=26.54 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=19.1
Q ss_pred CCCCCCCceeEecCCcceeEecccccc
Q 043865 117 ARRPACGSCVERKEGCRVMYCRCKTSF 143 (203)
Q Consensus 117 k~CP~C~~~iek~~GCnhm~C~C~~~F 143 (203)
-+||.|+......+ +...|..+|+|
T Consensus 3 ~~CP~C~~~l~~~~--~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTLEE--NSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcchhcCC--CEEEcCCCCCC
Confidence 36999999996644 56888667776
No 316
>PF15168 TRIQK: Triple QxxK/R motif-containing protein family
Probab=20.56 E-value=1.7e+02 Score=19.49 Aligned_cols=9 Identities=11% Similarity=0.460 Sum_probs=4.2
Q ss_pred HHHHHHhhh
Q 043865 189 GVIYGIYCV 197 (203)
Q Consensus 189 ~~~~~~~~~ 197 (203)
+.+|+++++
T Consensus 63 ~a~Ya~fyl 71 (79)
T PF15168_consen 63 LAFYAFFYL 71 (79)
T ss_pred HHHHHHHHH
Confidence 345555443
No 317
>PF07123 PsbW: Photosystem II reaction centre W protein (PsbW); InterPro: IPR009806 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbW found in PSII, where it is a subunit of the oxygen-evolving complex. PsbW appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of PsbW, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 2 PsbW.; GO: 0015979 photosynthesis, 0009507 chloroplast, 0009523 photosystem II
Probab=20.39 E-value=1e+02 Score=23.03 Aligned_cols=19 Identities=37% Similarity=0.731 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHH--HHHHh
Q 043865 177 LILIFTVLGVLGGV--IYGIY 195 (203)
Q Consensus 177 ~~~~f~~l~~~~~~--~~~~~ 195 (203)
.+|-||++++++++ +|.+|
T Consensus 104 ~~LgwIL~gVf~lIWslY~~~ 124 (138)
T PF07123_consen 104 NLLGWILLGVFGLIWSLYFVY 124 (138)
T ss_pred chhHHHHHHHHHHHHHHHHhh
Confidence 35667777777654 45444
No 318
>PF12113 SVM_signal: SVM protein signal sequence; InterPro: IPR021970 This domain is presumed to be a signal peptide sequence found in Sequence-variable mosaic (SVM) proteins []. It is found in phytoplasmas. This presumed signal sequence is about 30 amino acids in length.
Probab=20.22 E-value=1e+02 Score=17.10 Aligned_cols=11 Identities=36% Similarity=0.809 Sum_probs=5.9
Q ss_pred HHHHHHHHHHH
Q 043865 177 LILIFTVLGVL 187 (203)
Q Consensus 177 ~~~~f~~l~~~ 187 (203)
.+.+|++|+++
T Consensus 12 ~i~Lf~~LGL~ 22 (33)
T PF12113_consen 12 NIFLFIFLGLF 22 (33)
T ss_pred hhHHHHHHHHH
Confidence 45555555554
No 319
>PF13214 DUF4022: Protein of unknown function (DUF4022)
Probab=20.19 E-value=2e+02 Score=18.68 Aligned_cols=17 Identities=18% Similarity=0.362 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHhhhhh
Q 043865 183 VLGVLGGVIYGIYCVIK 199 (203)
Q Consensus 183 ~l~~~~~~~~~~~~~~~ 199 (203)
--|++|+.+-|.|+++.
T Consensus 63 t~silgl~~apayfflq 79 (83)
T PF13214_consen 63 TASILGLCVAPAYFFLQ 79 (83)
T ss_pred HHHHHHHHHhHHHHHHH
Confidence 34788888888888764
No 320
>PF11375 DUF3177: Protein of unknown function (DUF3177); InterPro: IPR021515 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Probab=20.18 E-value=90 Score=24.63 Aligned_cols=14 Identities=29% Similarity=0.612 Sum_probs=6.3
Q ss_pred HHHHHHHHHHhhhh
Q 043865 185 GVLGGVIYGIYCVI 198 (203)
Q Consensus 185 ~~~~~~~~~~~~~~ 198 (203)
+++.+++|-+|.++
T Consensus 165 ~LviY~~yl~~fll 178 (190)
T PF11375_consen 165 GLVIYVLYLLYFLL 178 (190)
T ss_pred HHHHHHHHHHHHHH
Confidence 33334444445444
No 321
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=20.03 E-value=36 Score=29.25 Aligned_cols=26 Identities=35% Similarity=0.862 Sum_probs=21.6
Q ss_pred CCCceeCCCccccccccCCcCCCCCC
Q 043865 66 TLKKARCPNCKQWFCFQCKVAWHAGY 91 (203)
Q Consensus 66 ~~~~~~C~~C~~~~C~~C~~~~H~~~ 91 (203)
.....+|+.|+..||..|..-.|+-+
T Consensus 342 ~~~~y~C~~Ck~~FCldCDv~iHesL 367 (378)
T KOG2807|consen 342 SSGRYRCESCKNVFCLDCDVFIHESL 367 (378)
T ss_pred CCCcEEchhccceeeccchHHHHhhh
Confidence 35678999999999999988877654
No 322
>PF15106 TMEM156: TMEM156 protein family
Probab=20.02 E-value=1.8e+02 Score=23.50 Aligned_cols=27 Identities=30% Similarity=0.520 Sum_probs=14.0
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043865 167 CHHYCAIISGLILIFTVLGVLGGVIYGIY 195 (203)
Q Consensus 167 ~~~~~~~~~~~~~~f~~l~~~~~~~~~~~ 195 (203)
|.++.+--++.+|.|++|.++ +||=|.
T Consensus 172 CsmKITWYvLVllVfiflii~--iI~KIl 198 (226)
T PF15106_consen 172 CSMKITWYVLVLLVFIFLIIL--IIYKIL 198 (226)
T ss_pred eehhhHHHHHHHHHHHHHHHH--HHHHHH
Confidence 555555555555555555443 455444
No 323
>TIGR00327 secE_euk_arch protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic. This model describes archaeal SEC61-like and eukaryotic SEC61 but not bacterial secE proteins, for which a Pfam pfam00584 (SecE) has been created.
Probab=20.00 E-value=2.5e+02 Score=17.85 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhh
Q 043865 178 ILIFTVLGVLGGVIYGIYCVIKR 200 (203)
Q Consensus 178 ~~~f~~l~~~~~~~~~~~~~~~~ 200 (203)
.+=|++++++|.+|+-+...|.-
T Consensus 36 ~iG~~i~G~IGf~Ikli~~pi~~ 58 (61)
T TIGR00327 36 GIGIIIVGIIGYIIKIIAIPIRG 58 (61)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Confidence 34467778888777666555543
Done!