Query 029839
Match_columns 187
No_of_seqs 115 out of 684
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 04:28:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029839.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029839hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1984 Vesicle coat complex C 100.0 2.9E-50 6.3E-55 372.0 14.6 169 18-186 268-452 (1007)
2 KOG1985 Vesicle coat complex C 100.0 1.2E-43 2.6E-48 327.2 11.3 154 31-187 164-330 (887)
3 COG5028 Vesicle coat complex C 100.0 3.1E-43 6.7E-48 322.6 11.0 167 18-187 132-312 (861)
4 PLN00162 transport protein sec 100.0 9.4E-37 2E-41 288.5 14.8 142 35-187 7-157 (761)
5 PTZ00395 Sec24-related protein 100.0 3.5E-33 7.7E-38 268.1 12.5 136 4-144 622-788 (1560)
6 KOG1986 Vesicle coat complex C 99.9 6.2E-28 1.3E-32 220.5 8.6 141 33-187 5-154 (745)
7 COG5047 SEC23 Vesicle coat com 99.9 2.4E-25 5.1E-30 200.3 9.3 140 34-187 6-155 (755)
8 PF04810 zf-Sec23_Sec24: Sec23 99.5 3.3E-15 7.1E-20 91.7 1.9 34 87-120 1-34 (40)
9 PRK00398 rpoP DNA-directed RNA 88.0 0.44 9.6E-06 29.4 2.1 28 88-119 3-30 (46)
10 PF13719 zinc_ribbon_5: zinc-r 86.5 0.45 9.7E-06 28.2 1.4 31 88-118 2-33 (37)
11 PF09723 Zn-ribbon_8: Zinc rib 80.5 0.85 1.8E-05 27.7 0.9 30 89-119 6-35 (42)
12 smart00661 RPOL9 RNA polymeras 79.3 1.1 2.3E-05 28.0 1.2 27 90-118 2-28 (52)
13 cd00350 rubredoxin_like Rubred 78.8 1.4 3E-05 25.3 1.4 24 90-119 3-26 (33)
14 COG2888 Predicted Zn-ribbon RN 77.8 0.85 1.8E-05 30.1 0.4 12 84-95 34-45 (61)
15 PF08271 TF_Zn_Ribbon: TFIIB z 76.5 2.5 5.4E-05 25.6 2.2 26 90-118 2-27 (43)
16 PF02318 FYVE_2: FYVE-type zin 75.5 1.8 3.8E-05 32.2 1.6 32 87-118 70-102 (118)
17 TIGR00100 hypA hydrogenase nic 74.6 2 4.3E-05 31.9 1.6 30 86-121 68-97 (115)
18 smart00834 CxxC_CXXC_SSSS Puta 74.6 1.6 3.4E-05 25.8 0.9 29 89-118 6-34 (41)
19 PRK12380 hydrogenase nickel in 74.3 2 4.3E-05 31.8 1.6 29 86-120 68-96 (113)
20 PF09082 DUF1922: Domain of un 74.1 3.5 7.6E-05 28.0 2.6 25 88-118 3-27 (68)
21 cd00730 rubredoxin Rubredoxin; 74.1 1.4 2.9E-05 28.1 0.6 30 90-119 3-43 (50)
22 PF13717 zinc_ribbon_4: zinc-r 72.4 2.2 4.8E-05 25.1 1.2 30 89-118 3-33 (36)
23 PRK03681 hypA hydrogenase nick 71.4 2.5 5.5E-05 31.3 1.6 30 86-121 68-98 (114)
24 smart00401 ZnF_GATA zinc finge 71.2 2.3 4.9E-05 27.1 1.1 31 88-118 3-33 (52)
25 PF14803 Nudix_N_2: Nudix N-te 70.6 1.2 2.6E-05 26.1 -0.3 28 91-118 3-30 (34)
26 PF08792 A2L_zn_ribbon: A2L zi 69.9 7 0.00015 22.6 2.9 28 87-118 2-29 (33)
27 TIGR02605 CxxC_CxxC_SSSS putat 69.8 2.2 4.8E-05 26.7 0.8 30 89-119 6-35 (52)
28 PF11781 RRN7: RNA polymerase 69.4 3.4 7.4E-05 24.4 1.5 26 88-118 8-33 (36)
29 TIGR03788 marine_srt_targ mari 69.4 7.2 0.00016 36.6 4.5 38 148-186 268-305 (596)
30 PRK03954 ribonuclease P protei 68.8 4.1 8.9E-05 30.7 2.2 31 89-119 65-102 (121)
31 PF13240 zinc_ribbon_2: zinc-r 67.6 2 4.4E-05 22.8 0.2 13 90-102 1-13 (23)
32 COG1096 Predicted RNA-binding 66.4 4.1 8.9E-05 33.0 1.9 29 88-122 149-177 (188)
33 PRK00432 30S ribosomal protein 66.2 3.1 6.7E-05 26.4 0.9 24 89-118 21-45 (50)
34 PRK12722 transcriptional activ 65.4 2.8 6E-05 34.0 0.8 30 86-118 132-162 (187)
35 PF12760 Zn_Tnp_IS1595: Transp 65.2 7.7 0.00017 23.8 2.6 27 89-118 19-45 (46)
36 COG1996 RPC10 DNA-directed RNA 65.2 3.6 7.8E-05 26.1 1.1 27 88-118 6-32 (49)
37 TIGR01053 LSD1 zinc finger dom 64.1 5.2 0.00011 22.9 1.5 26 89-118 2-27 (31)
38 KOG3799 Rab3 effector RIM1 and 63.6 3.6 7.8E-05 31.8 1.0 27 88-118 89-115 (169)
39 PF07754 DUF1610: Domain of un 63.4 5.6 0.00012 21.5 1.5 24 91-118 1-24 (24)
40 PF10058 DUF2296: Predicted in 62.3 6.5 0.00014 25.3 1.9 33 86-118 20-52 (54)
41 PF00301 Rubredoxin: Rubredoxi 62.3 1.8 3.9E-05 27.2 -0.7 11 108-118 32-42 (47)
42 PF07282 OrfB_Zn_ribbon: Putat 62.3 5.2 0.00011 26.4 1.6 29 87-119 27-55 (69)
43 PRK00564 hypA hydrogenase nick 61.1 3.4 7.3E-05 30.8 0.5 30 86-121 69-99 (117)
44 PF00320 GATA: GATA zinc finge 60.8 2.4 5.2E-05 24.9 -0.3 28 91-118 1-28 (36)
45 PF03604 DNA_RNApol_7kD: DNA d 60.5 6 0.00013 22.8 1.4 13 85-97 14-26 (32)
46 COG2051 RPS27A Ribosomal prote 59.9 12 0.00025 25.3 2.8 28 88-118 19-46 (67)
47 TIGR02098 MJ0042_CXXC MJ0042 f 58.9 6.5 0.00014 22.9 1.4 30 89-118 3-33 (38)
48 TIGR01384 TFS_arch transcripti 56.5 7.1 0.00015 28.0 1.5 24 90-119 2-25 (104)
49 smart00132 LIM Zinc-binding do 56.3 9.6 0.00021 21.4 1.8 29 90-118 1-35 (39)
50 smart00659 RPOLCX RNA polymera 56.0 10 0.00022 23.4 1.9 24 90-118 4-27 (44)
51 PRK00415 rps27e 30S ribosomal 55.9 15 0.00032 24.2 2.8 28 88-118 11-38 (59)
52 PRK03824 hypA hydrogenase nick 55.1 7.6 0.00016 29.6 1.6 34 87-120 69-117 (135)
53 PF01927 Mut7-C: Mut7-C RNAse 54.0 10 0.00022 29.1 2.1 31 88-118 91-132 (147)
54 PF06943 zf-LSD1: LSD1 zinc fi 53.5 9.6 0.00021 20.8 1.4 23 91-117 1-23 (25)
55 TIGR00686 phnA alkylphosphonat 53.5 11 0.00024 27.8 2.1 26 88-118 2-27 (109)
56 PRK00762 hypA hydrogenase nick 52.6 6.4 0.00014 29.6 0.8 34 86-120 68-102 (124)
57 cd02342 ZZ_UBA_plant Zinc fing 52.1 9.4 0.0002 23.6 1.3 23 89-118 1-23 (43)
58 PRK14890 putative Zn-ribbon RN 52.0 11 0.00023 24.9 1.6 12 108-119 46-57 (59)
59 COG1545 Predicted nucleic-acid 51.8 27 0.00058 26.7 4.1 64 87-161 28-93 (140)
60 PF08274 PhnA_Zn_Ribbon: PhnA 51.6 8 0.00017 22.0 0.9 26 88-118 2-27 (30)
61 PF13408 Zn_ribbon_recom: Reco 51.4 9.6 0.00021 23.8 1.4 32 86-118 3-34 (58)
62 PF13831 PHD_2: PHD-finger; PD 51.4 2 4.3E-05 25.4 -1.8 32 86-117 2-36 (36)
63 PHA00626 hypothetical protein 51.1 15 0.00033 24.0 2.2 11 108-118 21-31 (59)
64 PF01155 HypA: Hydrogenase exp 49.0 4.2 9.2E-05 30.0 -0.7 29 86-120 68-96 (113)
65 PF06827 zf-FPG_IleRS: Zinc fi 48.0 9.6 0.00021 21.1 0.9 26 90-117 3-28 (30)
66 PRK00420 hypothetical protein; 46.2 15 0.00032 27.3 1.9 25 89-118 24-48 (112)
67 PF13894 zf-C2H2_4: C2H2-type 45.9 10 0.00022 18.8 0.7 8 111-118 1-8 (24)
68 PF15288 zf-CCHC_6: Zinc knuck 45.3 7.9 0.00017 23.5 0.2 9 89-97 2-10 (40)
69 PRK14810 formamidopyrimidine-D 44.4 20 0.00043 30.4 2.6 28 89-118 245-272 (272)
70 PF10571 UPF0547: Uncharacteri 43.8 8.9 0.00019 20.9 0.3 21 90-118 2-22 (26)
71 TIGR00311 aIF-2beta translatio 43.5 27 0.00058 26.7 2.9 29 88-119 97-127 (133)
72 cd00202 ZnF_GATA Zinc finger D 43.2 4.3 9.3E-05 26.1 -1.2 29 90-118 1-29 (54)
73 PF09297 zf-NADH-PPase: NADH p 42.7 25 0.00054 19.7 2.1 25 90-118 5-29 (32)
74 COG1645 Uncharacterized Zn-fin 42.5 18 0.00039 27.7 1.8 24 89-118 29-52 (131)
75 PRK12860 transcriptional activ 42.1 13 0.00027 30.3 1.0 31 85-118 131-162 (189)
76 PF06677 Auto_anti-p27: Sjogre 42.1 23 0.00051 21.5 2.0 24 89-117 18-41 (41)
77 COG1998 RPS31 Ribosomal protei 41.9 15 0.00032 23.4 1.1 27 89-119 20-46 (51)
78 PRK12496 hypothetical protein; 41.9 11 0.00025 29.6 0.7 25 89-119 128-152 (164)
79 smart00778 Prim_Zn_Ribbon Zinc 41.8 23 0.00049 21.1 1.8 27 90-118 5-33 (37)
80 PF05280 FlhC: Flagellar trans 41.2 10 0.00022 30.4 0.3 31 85-118 131-162 (175)
81 cd00729 rubredoxin_SM Rubredox 41.0 14 0.00031 21.3 0.9 9 110-118 2-10 (34)
82 COG1592 Rubrerythrin [Energy p 40.6 14 0.00031 29.3 1.1 13 107-119 131-143 (166)
83 COG0675 Transposase and inacti 40.5 16 0.00034 30.7 1.4 25 86-119 307-331 (364)
84 COG3357 Predicted transcriptio 39.8 10 0.00023 27.2 0.2 28 87-118 57-84 (97)
85 PF04032 Rpr2: RNAse P Rpr2/Rp 39.5 12 0.00026 25.5 0.4 31 88-118 46-85 (85)
86 PRK10220 hypothetical protein; 39.3 24 0.00051 26.2 2.0 26 88-118 3-28 (111)
87 TIGR03436 acidobact_VWFA VWFA- 39.0 54 0.0012 27.5 4.5 32 150-183 52-83 (296)
88 PF02891 zf-MIZ: MIZ/SP-RING z 39.0 9.2 0.0002 24.1 -0.2 13 106-118 37-49 (50)
89 PF13453 zf-TFIIB: Transcripti 38.6 22 0.00047 21.2 1.4 11 87-97 18-28 (41)
90 PRK13685 hypothetical protein; 37.1 60 0.0013 28.0 4.5 36 151-186 88-127 (326)
91 PRK12286 rpmF 50S ribosomal pr 35.7 28 0.0006 22.6 1.7 25 86-119 25-49 (57)
92 PF12773 DZR: Double zinc ribb 35.6 13 0.00028 22.8 0.1 29 86-119 10-38 (50)
93 cd04931 ACT_PAH ACT domain of 35.0 61 0.0013 22.8 3.5 35 150-186 53-87 (90)
94 PF09943 DUF2175: Uncharacteri 35.0 21 0.00046 26.1 1.2 10 109-118 1-10 (101)
95 PF10263 SprT-like: SprT-like 35.0 22 0.00048 26.9 1.3 31 86-118 121-151 (157)
96 cd02344 ZZ_HERC2 Zinc finger, 34.9 25 0.00055 21.7 1.3 23 89-118 1-23 (45)
97 PRK08270 anaerobic ribonucleos 34.1 17 0.00037 34.9 0.7 25 86-119 624-648 (656)
98 PRK06393 rpoE DNA-directed RNA 34.0 16 0.00034 24.5 0.3 22 88-119 5-26 (64)
99 PLN00209 ribosomal protein S27 33.4 51 0.0011 23.4 2.8 28 88-118 36-63 (86)
100 PF12874 zf-met: Zinc-finger o 33.2 22 0.00048 18.2 0.8 8 111-118 1-8 (25)
101 PRK01103 formamidopyrimidine/5 32.9 40 0.00086 28.6 2.7 27 90-118 247-273 (274)
102 PF08879 WRC: WRC; InterPro: 32.2 21 0.00045 22.3 0.6 10 106-115 10-19 (46)
103 PF00130 C1_1: Phorbol esters/ 32.0 31 0.00067 21.2 1.4 28 86-118 9-36 (53)
104 TIGR01031 rpmF_bact ribosomal 31.9 30 0.00066 22.2 1.4 24 86-118 24-47 (55)
105 PF02150 RNA_POL_M_15KD: RNA p 31.9 56 0.0012 18.9 2.4 26 90-118 3-28 (35)
106 COG1571 Predicted DNA-binding 31.5 28 0.00062 31.7 1.6 29 86-119 348-376 (421)
107 COG0266 Nei Formamidopyrimidin 31.4 32 0.0007 29.5 1.9 29 88-118 245-273 (273)
108 PF02591 DUF164: Putative zinc 31.1 24 0.00051 22.4 0.8 13 86-98 44-56 (56)
109 COG2042 Uncharacterized conser 30.7 22 0.00048 28.4 0.7 46 25-73 12-60 (179)
110 smart00400 ZnF_CHCC zinc finge 30.4 72 0.0016 20.0 3.0 22 100-121 13-34 (55)
111 PF14952 zf-tcix: Putative tre 30.3 22 0.00048 22.0 0.5 12 86-97 9-20 (44)
112 PTZ00083 40S ribosomal protein 30.2 62 0.0014 22.9 2.8 28 88-118 35-62 (85)
113 TIGR00595 priA primosomal prot 30.2 23 0.00049 32.8 0.8 30 88-118 222-261 (505)
114 PRK11827 hypothetical protein; 29.7 42 0.00091 22.1 1.8 28 87-118 7-34 (60)
115 cd02340 ZZ_NBR1_like Zinc fing 29.6 36 0.00078 20.6 1.4 22 89-118 1-22 (43)
116 PRK08351 DNA-directed RNA poly 29.6 23 0.00049 23.5 0.5 20 90-119 5-24 (61)
117 COG1198 PriA Primosomal protei 28.1 2.7E+02 0.0058 27.4 7.6 81 88-177 444-530 (730)
118 PF01667 Ribosomal_S27e: Ribos 28.0 41 0.00089 21.8 1.5 27 89-118 8-34 (55)
119 COG0846 SIR2 NAD-dependent pro 28.0 33 0.00072 29.0 1.4 19 87-105 145-164 (250)
120 PRK10445 endonuclease VIII; Pr 27.9 53 0.0012 27.7 2.6 27 89-117 236-262 (263)
121 PF09779 Ima1_N: Ima1 N-termin 27.8 29 0.00063 26.2 0.9 29 89-119 1-29 (131)
122 COG2023 RPR2 RNase P subunit R 27.6 45 0.00099 24.5 1.8 30 89-118 57-90 (105)
123 PF14353 CpXC: CpXC protein 27.6 56 0.0012 24.1 2.5 11 109-119 37-47 (128)
124 PRK04351 hypothetical protein; 27.5 62 0.0013 25.1 2.7 31 86-118 110-140 (149)
125 PRK14892 putative transcriptio 27.3 47 0.001 24.1 1.9 33 86-119 19-51 (99)
126 COG2956 Predicted N-acetylgluc 27.2 30 0.00065 30.8 1.0 25 86-118 352-376 (389)
127 PRK13945 formamidopyrimidine-D 27.1 52 0.0011 28.0 2.4 27 89-117 255-281 (282)
128 cd02338 ZZ_PCMF_like Zinc fing 27.0 42 0.00091 20.9 1.4 23 89-118 1-23 (49)
129 TIGR00375 conserved hypothetic 26.8 18 0.00038 32.4 -0.5 56 84-144 236-301 (374)
130 PRK07562 ribonucleotide-diphos 26.8 50 0.0011 34.1 2.6 28 87-119 1189-1216(1220)
131 PF06007 PhnJ: Phosphonate met 26.7 36 0.00078 28.9 1.3 26 89-114 236-264 (277)
132 COG1773 Rubredoxin [Energy pro 26.6 38 0.00082 22.0 1.1 11 108-118 34-44 (55)
133 PF06524 NOA36: NOA36 protein; 26.3 39 0.00084 29.0 1.5 15 104-118 136-150 (314)
134 PF11672 DUF3268: Protein of u 26.1 44 0.00096 24.4 1.6 31 88-118 2-39 (102)
135 PRK07218 replication factor A; 26.0 34 0.00073 31.2 1.1 23 86-118 295-317 (423)
136 PF08273 Prim_Zn_Ribbon: Zinc- 25.9 33 0.00071 20.7 0.7 26 91-117 6-33 (40)
137 PRK14811 formamidopyrimidine-D 25.8 58 0.0013 27.6 2.5 27 90-118 237-263 (269)
138 PF04216 FdhE: Protein involve 25.5 49 0.0011 28.1 2.0 30 87-118 171-205 (290)
139 PRK00423 tfb transcription ini 25.3 70 0.0015 27.6 2.9 30 86-118 9-38 (310)
140 COG1439 Predicted nucleic acid 24.9 37 0.00081 27.3 1.1 26 86-119 137-162 (177)
141 PF06858 NOG1: Nucleolar GTP-b 24.5 1.4E+02 0.003 19.6 3.5 32 150-183 13-47 (58)
142 PF05191 ADK_lid: Adenylate ki 24.3 26 0.00055 20.6 0.0 26 91-118 4-29 (36)
143 KOG1074 Transcriptional repres 23.7 29 0.00063 34.3 0.3 35 84-118 349-389 (958)
144 PF05741 zf-nanos: Nanos RNA b 23.6 24 0.00053 22.9 -0.2 14 109-122 32-45 (55)
145 PF00025 Arf: ADP-ribosylation 23.5 1.6E+02 0.0034 22.6 4.4 29 150-182 81-109 (175)
146 PRK12336 translation initiatio 23.4 88 0.0019 25.4 3.0 29 88-119 98-128 (201)
147 PF13465 zf-H2C2_2: Zinc-finge 23.1 51 0.0011 17.4 1.1 12 107-118 11-22 (26)
148 KOG3507 DNA-directed RNA polym 23.0 37 0.00079 22.4 0.6 11 86-96 35-45 (62)
149 PHA02942 putative transposase; 22.8 49 0.0011 29.6 1.5 28 87-119 324-351 (383)
150 COG1656 Uncharacterized conser 22.7 39 0.00084 26.9 0.8 70 49-118 54-138 (165)
151 PRK05333 NAD-dependent deacety 22.6 46 0.001 28.3 1.3 19 87-105 178-196 (285)
152 TIGR00354 polC DNA polymerase, 22.2 40 0.00088 33.9 0.9 23 86-118 623-645 (1095)
153 PF01873 eIF-5_eIF-2B: Domain 22.1 72 0.0016 24.0 2.1 28 88-118 93-122 (125)
154 cd01411 SIR2H SIR2H: Uncharact 22.1 57 0.0012 26.7 1.7 15 89-103 137-151 (225)
155 PRK05452 anaerobic nitric oxid 22.1 41 0.0009 30.9 0.9 34 86-119 423-467 (479)
156 COG3677 Transposase and inacti 22.0 40 0.00086 25.5 0.7 33 87-119 29-62 (129)
157 smart00290 ZnF_UBP Ubiquitin C 22.0 62 0.0013 19.6 1.5 19 90-118 1-19 (50)
158 COG1594 RPB9 DNA-directed RNA 21.8 65 0.0014 23.8 1.8 28 89-118 3-30 (113)
159 TIGR00577 fpg formamidopyrimid 21.7 78 0.0017 26.8 2.5 26 90-117 247-272 (272)
160 smart00249 PHD PHD zinc finger 21.7 56 0.0012 18.7 1.2 32 85-116 11-47 (47)
161 COG2093 DNA-directed RNA polym 21.3 34 0.00074 22.8 0.2 22 90-119 6-27 (64)
162 COG1240 ChlD Mg-chelatase subu 21.3 1.3E+02 0.0028 25.7 3.7 34 149-182 76-109 (261)
163 PF06397 Desulfoferrod_N: Desu 21.2 46 0.001 19.7 0.7 12 107-118 3-14 (36)
164 PRK03988 translation initiatio 21.0 1.1E+02 0.0025 23.4 3.0 29 88-119 102-132 (138)
165 PRK07111 anaerobic ribonucleos 20.9 43 0.00094 32.7 0.8 24 86-118 678-701 (735)
166 PF12172 DUF35_N: Rubredoxin-l 20.5 59 0.0013 18.6 1.1 24 87-118 10-33 (37)
167 PTZ00441 sporozoite surface pr 20.4 1.1E+02 0.0023 29.2 3.3 36 150-185 41-76 (576)
168 PRK14873 primosome assembly pr 20.4 75 0.0016 30.7 2.3 30 87-118 391-430 (665)
169 PF14599 zinc_ribbon_6: Zinc-r 20.2 44 0.00095 22.1 0.5 10 88-97 48-57 (61)
170 KOG0936 Clathrin adaptor compl 20.1 1.4E+02 0.0031 23.6 3.4 30 150-182 69-98 (182)
171 COG0375 HybF Zn finger protein 20.1 67 0.0014 24.0 1.5 31 86-122 68-98 (115)
172 PF00096 zf-C2H2: Zinc finger, 20.0 54 0.0012 16.3 0.8 8 111-118 1-8 (23)
No 1
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.9e-50 Score=372.04 Aligned_cols=169 Identities=53% Similarity=1.083 Sum_probs=163.3
Q ss_pred CCCCCCcceeEecCCCCCCCCeeEeeccccCCCHHHhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeE
Q 029839 18 KPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGY 97 (187)
Q Consensus 18 ~~pp~~~~~~~~~d~gn~~p~~iR~T~~~~P~~~~~~~~~~iPlgi~v~Pf~~~~~~e~~ip~v~~~~~~~~RC~~C~ay 97 (187)
.+||++||+|++.|||||+|+|||+|+|+||.|.++++.++||||++|+||+.+.+.|+++|+||+++.+++||++|+||
T Consensus 268 ~~PPl~TTd~~~~DqGN~sPr~mr~T~Y~iP~T~Dl~~as~iPLalvIqPfa~l~p~E~~~~vVd~g~sgPvRC~RCkaY 347 (1007)
T KOG1984|consen 268 QPPPLVTTDFFIQDQGNCSPRFMRCTMYTIPCTNDLLKASQIPLALVIQPFATLTPNEAPVPVVDLGESGPVRCNRCKAY 347 (1007)
T ss_pred CCCCCcccceEEeccCCCCcchheeecccCCccHhHHHhcCCcceeEecccccCCcccCCCceecCCCCCCcchhhhhhh
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcCceEEEeCCceEEEecCCC--------------CCcccCCCCCCccCCccEEEEechhhhcc--CCCCcEEEEEEEcc
Q 029839 98 RNPFMEFVDNGKSFVCNFCGL--------------DGRCLDADERPELCRGTVEFAASREFMMR--NVMPPVYFFLIDVS 161 (187)
Q Consensus 98 iNp~~~~~~~g~~w~C~~C~~--------------~~~~~~~~~~pEL~~~tvE~~~p~~y~~r--~~~pp~~vFvID~s 161 (187)
+|||++|+++|++|+||||+. +++|.|.+.||||..|+|||+++++|+.+ .+.||+|||+||||
T Consensus 348 inPFmqF~~~gr~f~Cn~C~~~n~vp~~yf~~L~~~grr~D~~erpEL~~Gt~dfvatk~Y~~~~k~p~ppafvFmIDVS 427 (1007)
T KOG1984|consen 348 INPFMQFIDGGRKFICNFCGSKNQVPDDYFNHLGPTGRRVDVEERPELCLGTVDFVATKDYCRKTKPPKPPAFVFMIDVS 427 (1007)
T ss_pred cCcceEEecCCceEEecCCCccccCChhhcccCCCcccccccccCchhcccccceeeehhhhhcCCCCCCceEEEEEEee
Confidence 999999999999999999998 25678999999999999999999999987 89999999999999
Q ss_pred hhhHhhcHHHHHHHHHHHHHhcCCC
Q 029839 162 TDAVQTGATAAACSAIMQVISDLPV 186 (187)
Q Consensus 162 ~~~~~~g~l~~~~~sL~~~L~~lP~ 186 (187)
++++++|++.+++++|++.|+.||.
T Consensus 428 y~Ai~~G~~~a~ce~ik~~l~~lp~ 452 (1007)
T KOG1984|consen 428 YNAISNGAVKAACEAIKSVLEDLPR 452 (1007)
T ss_pred hhhhhcchHHHHHHHHHHHHhhcCc
Confidence 9999999999999999999999985
No 2
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.2e-43 Score=327.24 Aligned_cols=154 Identities=43% Similarity=0.796 Sum_probs=143.1
Q ss_pred CCCCCCCCeeEeeccccCCCHHHhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeEEcCceEEEeCCce
Q 029839 31 DTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKS 110 (187)
Q Consensus 31 d~gn~~p~~iR~T~~~~P~~~~~~~~~~iPlgi~v~Pf~~~~~~e~~ip~v~~~~~~~~RC~~C~ayiNp~~~~~~~g~~ 110 (187)
+..||+|+|+|+|++.||.+++++++++||||++|+||+++. +..++|++. ...|+||++||+|||||+.|++.|++
T Consensus 164 ~~~nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~-d~~~~p~~~--~~~IvRCr~CRtYiNPFV~fid~gr~ 240 (887)
T KOG1985|consen 164 ESSNCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLD-DIDPLPVIT--STLIVRCRRCRTYINPFVEFIDQGRR 240 (887)
T ss_pred cccCCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeeccccc-ccCCCCccc--CCceeeehhhhhhcCCeEEecCCCce
Confidence 568999999999999999999999999999999999999887 334566655 67899999999999999999999999
Q ss_pred EEEecCCCC-------------CcccCCCCCCccCCccEEEEechhhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHH
Q 029839 111 FVCNFCGLD-------------GRCLDADERPELCRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAI 177 (187)
Q Consensus 111 w~C~~C~~~-------------~~~~~~~~~pEL~~~tvE~~~p~~y~~r~~~pp~~vFvID~s~~~~~~g~l~~~~~sL 177 (187)
|+||+|+.. +.+.|+.+||||++++|||++|.||+.|+|+|++|||+||||..++|+|+|++++++|
T Consensus 241 WrCNlC~~~NdvP~~f~~~~~t~~~~~~~~RpEl~~s~vE~iAP~eYmlR~P~Pavy~FliDVS~~a~ksG~L~~~~~sl 320 (887)
T KOG1985|consen 241 WRCNLCGRVNDVPDDFDWDPLTGAYGDPYSRPELTSSVVEFIAPSEYMLRPPQPAVYVFLIDVSISAIKSGYLETVARSL 320 (887)
T ss_pred eeechhhhhcCCcHHhhcCccccccCCcccCccccceeEEEecCcccccCCCCCceEEEEEEeehHhhhhhHHHHHHHHH
Confidence 999999992 3467899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCCC
Q 029839 178 MQVISDLPVF 187 (187)
Q Consensus 178 ~~~L~~lP~~ 187 (187)
++.||.||++
T Consensus 321 L~~LD~lpgd 330 (887)
T KOG1985|consen 321 LENLDALPGD 330 (887)
T ss_pred HHhhhcCCCC
Confidence 9999999964
No 3
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=3.1e-43 Score=322.59 Aligned_cols=167 Identities=40% Similarity=0.809 Sum_probs=154.0
Q ss_pred CCCCCCcceeEecCCCCCCCCeeEeeccccCCCHHHhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeE
Q 029839 18 KPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGY 97 (187)
Q Consensus 18 ~~pp~~~~~~~~~d~gn~~p~~iR~T~~~~P~~~~~~~~~~iPlgi~v~Pf~~~~~~e~~ip~v~~~~~~~~RC~~C~ay 97 (187)
..||+ ++.++..+++||+|+|+|+|+|++|.+.+++++++||||++|+||.++-+.+.++|+++ +..|+||++||+|
T Consensus 132 ~~ppl-tt~~~~~e~~n~~p~yvrsT~yaiP~t~dl~~~skiPfgLVI~Pf~~l~~e~~~vpl~~--d~~ivRCrrCrsY 208 (861)
T COG5028 132 IVPPL-TTNFVGSEQSNCSPKYVRSTMYAIPETNDLLKKSKIPFGLVIRPFLELYPEEDPVPLVE--DGSIVRCRRCRSY 208 (861)
T ss_pred CCCCc-ccceeeeccCCCCHHHHHHHHhhCCCchhHHHhcCCCceEEeehhhhcCccCCCCccCC--CCcchhhhhhHhh
Confidence 35666 99999999999999999999999999999999999999999999999888777788876 3448999999999
Q ss_pred EcCceEEEeCCceEEEecCCCCC--------------cccCCCCCCccCCccEEEEechhhhccCCCCcEEEEEEEcchh
Q 029839 98 RNPFMEFVDNGKSFVCNFCGLDG--------------RCLDADERPELCRGTVEFAASREFMMRNVMPPVYFFLIDVSTD 163 (187)
Q Consensus 98 iNp~~~~~~~g~~w~C~~C~~~~--------------~~~~~~~~pEL~~~tvE~~~p~~y~~r~~~pp~~vFvID~s~~ 163 (187)
+|||.+|+++|++|+||+|+..+ .|.|+..|+||.+++|||++|++|+.|.+.|++|||+||||..
T Consensus 209 iNPfv~fi~~g~kw~CNiC~~kN~vp~~~~~~~~~~~~r~d~~~r~El~~~vvdf~ap~~Y~~~~p~P~~yvFlIDVS~~ 288 (861)
T COG5028 209 INPFVQFIEQGRKWRCNICRSKNDVPEGFDNPSGPNDPRSDRYSRPELKSGVVDFLAPKEYSLRQPPPPVYVFLIDVSFE 288 (861)
T ss_pred cCceEEEecCCcEEEEeeccccccCcccccCcCCCCCccccccccchhhceeeEEecccceeeccCCCCEEEEEEEeehH
Confidence 99999999999999999999832 2456889999999999999999999999999999999999999
Q ss_pred hHhhcHHHHHHHHHHHHHhcCCCC
Q 029839 164 AVQTGATAAACSAIMQVISDLPVF 187 (187)
Q Consensus 164 ~~~~g~l~~~~~sL~~~L~~lP~~ 187 (187)
++++|++.++.++|++.|+.+|++
T Consensus 289 a~~~g~~~a~~r~Il~~l~~~~~~ 312 (861)
T COG5028 289 AIKNGLVKAAIRAILENLDQIPNF 312 (861)
T ss_pred hhhcchHHHHHHHHHhhccCCCCC
Confidence 999999999999999999999763
No 4
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=9.4e-37 Score=288.51 Aligned_cols=142 Identities=25% Similarity=0.337 Sum_probs=127.6
Q ss_pred CCCCeeEeeccccCCCHHHhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeEEcCceEEEeCCceEEEe
Q 029839 35 CSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFVCN 114 (187)
Q Consensus 35 ~~p~~iR~T~~~~P~~~~~~~~~~iPlgi~v~Pf~~~~~~e~~ip~v~~~~~~~~RC~~C~ayiNp~~~~~~~g~~w~C~ 114 (187)
.+-++||+|||+||.++.++++++|||||+||||++.. ++|+++ .+|+||++|+|||||||+|+.+|++|+||
T Consensus 7 e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~----~vp~v~---~~pvRC~~CraylNPf~~~d~~~~~W~C~ 79 (761)
T PLN00162 7 EAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLP----ELPVLP---YDPLRCRTCRAVLNPYCRVDFQAKIWICP 79 (761)
T ss_pred cccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCC----CCCcCC---CCCCccCCCcCEECCceEEecCCCEEEcc
Confidence 46689999999999999999999999999999999864 388887 57999999999999999999999999999
Q ss_pred cCCCCCc----c---cCCCCCCcc--CCccEEEEechhhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC
Q 029839 115 FCGLDGR----C---LDADERPEL--CRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP 185 (187)
Q Consensus 115 ~C~~~~~----~---~~~~~~pEL--~~~tvE~~~p~~y~~r~~~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~~lP 185 (187)
||+..|. + .+.+.+||| +++||||++|. |+.+++.||+|+||||+|..+++ ++.++++|+++|+.||
T Consensus 80 ~C~~~N~~P~~Y~~~~~~~~p~EL~p~~~TvEY~~p~-~~~~~~~pp~fvFvID~s~~~~~---l~~lk~sl~~~L~~LP 155 (761)
T PLN00162 80 FCFQRNHFPPHYSSISETNLPAELFPQYTTVEYTLPP-GSGGAPSPPVFVFVVDTCMIEEE---LGALKSALLQAIALLP 155 (761)
T ss_pred CCCCCCCCchHhcccCccCCChhhcCCceeEEEECCC-CCCCCCCCcEEEEEEecchhHHH---HHHHHHHHHHHHHhCC
Confidence 9999643 1 235678999 89999999998 88889999999999999999887 6667899999999999
Q ss_pred CC
Q 029839 186 VF 187 (187)
Q Consensus 186 ~~ 187 (187)
++
T Consensus 156 ~~ 157 (761)
T PLN00162 156 EN 157 (761)
T ss_pred CC
Confidence 74
No 5
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=3.5e-33 Score=268.09 Aligned_cols=136 Identities=29% Similarity=0.475 Sum_probs=113.1
Q ss_pred CCceEEeccCCCCcCCCCCCcceeEecCCCCCCCCeeEeeccccCCCHHHhhhcCCceEEEEecCCCCCCCCCCCceecc
Q 029839 4 SSVILYETRQGKSVKPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDF 83 (187)
Q Consensus 4 ~~~~~~~t~~~~~~~~pp~~~~~~~~~d~gn~~p~~iR~T~~~~P~~~~~~~~~~iPlgi~v~Pf~~~~~~e~~ip~v~~ 83 (187)
....+|+|+++. .||+.+++|+++|+|||+|+|||+|||.||.+.++++.+.|||||+|+||+.+.++| .||.++.
T Consensus 622 ~~~~~~~t~k~~---~pp~~~~~~~~~dtgn~dP~~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~e-~~~~~~~ 697 (1560)
T PTZ00395 622 KNLKVFETCKYI---SPPSYYQPYISIDTGKADPRFLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEGE-GIDKIDM 697 (1560)
T ss_pred ccchhhhhccCC---CCCCCCCceEEeecCCCChhhhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCCC-CCcccch
Confidence 456789999764 479999999999999999999999999999999999999999999999999988765 4888876
Q ss_pred C--------CCCceecCCCCeEEcCceEEEeCCceEEEecCCCCCc------------------c-cCCC----CCCccC
Q 029839 84 G--------ESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGR------------------C-LDAD----ERPELC 132 (187)
Q Consensus 84 ~--------~~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~~------------------~-~~~~----~~pEL~ 132 (187)
. ..+++||.+|++|+|+++.++.. ++++|+||++... + .+.+ -.--|.
T Consensus 698 ~~~~~d~~~~~~~~rc~~c~~y~~~~~~~~~~-~~~~c~~c~~~~~i~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 776 (1560)
T PTZ00395 698 KDIINDKEENIEILRCPKCLGYLHATILEDIS-SSVQCVFCDTDFLINENVLFDIFQYNEKIGHKESDHNEHGNSLSPLL 776 (1560)
T ss_pred hhcccchhhccceeecchhHhhhcchheeccc-ceEEEEecCCcchhhHHHHHHHHHHhhhhccccccccccccccchhh
Confidence 4 24799999999999999998865 7899999999321 1 1111 112467
Q ss_pred CccEEEEechhh
Q 029839 133 RGTVEFAASREF 144 (187)
Q Consensus 133 ~~tvE~~~p~~y 144 (187)
+|+||+++|+-|
T Consensus 777 ~~~~~~~~~~~~ 788 (1560)
T PTZ00395 777 KGSVDIIIPPIY 788 (1560)
T ss_pred cCceeEEccchh
Confidence 899999998765
No 6
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.95 E-value=6.2e-28 Score=220.49 Aligned_cols=141 Identities=27% Similarity=0.400 Sum_probs=122.7
Q ss_pred CCCCCCeeEeeccccCCCHHHhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCCCCeEEcCceEEEeCCceEE
Q 029839 33 GNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFV 112 (187)
Q Consensus 33 gn~~p~~iR~T~~~~P~~~~~~~~~~iPlgi~v~Pf~~~~~~e~~ip~v~~~~~~~~RC~~C~ayiNp~~~~~~~g~~w~ 112 (187)
.+..-++||+|||+||+++....++++|++++++||++... +|.+. ++|+||++|+||+||||+++.+.+.|.
T Consensus 5 ~~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~~~----~~~~~---y~P~~C~~C~AvlNPyc~vd~~a~~W~ 77 (745)
T KOG1986|consen 5 DIEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKERPD----LPPIQ---YDPLRCSKCGAVLNPYCSVDFRAKSWI 77 (745)
T ss_pred ccccCCCcccccccCCCcccccccccccHHHhccccccCCC----CCccC---CCCchhccchhhcCcceeecccCceEe
Confidence 46778999999999999999999999999999999997543 56665 899999999999999999999999999
Q ss_pred EecCCCCCc----c---cCCCCCCcc--CCccEEEEechhhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc
Q 029839 113 CNFCGLDGR----C---LDADERPEL--CRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD 183 (187)
Q Consensus 113 C~~C~~~~~----~---~~~~~~pEL--~~~tvE~~~p~~y~~r~~~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~~ 183 (187)
|+||..+|. + .+.+..+|| ++.+|||++++. ...||+|+||||++..+.+ |+.++++|+.+|+.
T Consensus 78 CpfC~qrN~~p~~Y~~is~~n~P~el~Pq~stvEy~l~~~----~~~ppvf~fVvDtc~~eee---L~~LkssL~~~l~l 150 (745)
T KOG1986|consen 78 CPFCNQRNPFPPHYSGISENNLPPELLPQYSTVEYTLSPG----RVSPPVFVFVVDTCMDEEE---LQALKSSLKQSLSL 150 (745)
T ss_pred ccccccCCCCChhhcccCccCCChhhcCCcceeEEecCCC----CCCCceEEEEEeeccChHH---HHHHHHHHHHHHhh
Confidence 999999652 2 234556688 789999999964 3459999999999998855 89999999999999
Q ss_pred CCCC
Q 029839 184 LPVF 187 (187)
Q Consensus 184 lP~~ 187 (187)
||++
T Consensus 151 LP~~ 154 (745)
T KOG1986|consen 151 LPEN 154 (745)
T ss_pred CCCc
Confidence 9985
No 7
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=99.92 E-value=2.4e-25 Score=200.31 Aligned_cols=140 Identities=26% Similarity=0.443 Sum_probs=121.7
Q ss_pred CCCCCeeEeeccccCCCHHHhhhcCCceEEEEecCCCCCCCCCCCceeccCCCCceecCC-CCeEEcCceEEEeCCceEE
Q 029839 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC-CRGYRNPFMEFVDNGKSFV 112 (187)
Q Consensus 34 n~~p~~iR~T~~~~P~~~~~~~~~~iPlgi~v~Pf~~~~~~e~~ip~v~~~~~~~~RC~~-C~ayiNp~~~~~~~g~~w~ 112 (187)
+.+-++||+|||+||.++.++.++.+|++++|+||++.+. +++. .++|+.|.. |+||+||||.++.+.+.|+
T Consensus 6 iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~~~----~~v~---~yepv~C~~pC~avlnpyC~id~r~~~W~ 78 (755)
T COG5047 6 IEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHEDDA----LTVN---YYEPVKCTAPCKAVLNPYCHIDERNQSWI 78 (755)
T ss_pred hccccceEEEEecccCCccccccccccHHHhccccccccc----cCcc---cCCCceecccchhhcCcceeeccCCceEe
Confidence 5678999999999999999999999999999999998643 4443 488999999 9999999999999999999
Q ss_pred EecCCCCCc----cc---CCCCCCcc--CCccEEEEechhhhccCCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc
Q 029839 113 CNFCGLDGR----CL---DADERPEL--CRGTVEFAASREFMMRNVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD 183 (187)
Q Consensus 113 C~~C~~~~~----~~---~~~~~pEL--~~~tvE~~~p~~y~~r~~~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~~ 183 (187)
|+||+.++. +. +.+..+|| ++.||||++++. ...||+|+||||++.+..+ +.+++++|...|..
T Consensus 79 CpfCnqrn~lp~qy~~iS~~~LplellpqssTiey~lskp----~~~ppvf~fvvD~~~D~e~---l~~Lkdslivslsl 151 (755)
T COG5047 79 CPFCNQRNTLPPQYRDISNANLPLELLPQSSTIEYTLSKP----VILPPVFFFVVDACCDEEE---LTALKDSLIVSLSL 151 (755)
T ss_pred cceecCCCCCChhhcCCCcccCCccccCCCceEEEEccCC----ccCCceEEEEEEeecCHHH---HHHHHHHHHHHHhc
Confidence 999999652 22 34566788 799999999874 5689999999999997655 89999999999999
Q ss_pred CCCC
Q 029839 184 LPVF 187 (187)
Q Consensus 184 lP~~ 187 (187)
||++
T Consensus 152 lppe 155 (755)
T COG5047 152 LPPE 155 (755)
T ss_pred CCcc
Confidence 9975
No 8
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=99.52 E-value=3.3e-15 Score=91.70 Aligned_cols=34 Identities=56% Similarity=1.255 Sum_probs=24.5
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~ 120 (187)
+|+||++|+||||||++|+.+|++|+|+||++.+
T Consensus 1 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 1 GPVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKN 34 (40)
T ss_dssp -S-B-TTT--BS-TTSEEETTTTEEEETTT--EE
T ss_pred CccccCCCCCEECCcceEcCCCCEEECcCCCCcC
Confidence 4899999999999999999999999999999843
No 9
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.99 E-value=0.44 Score=29.42 Aligned_cols=28 Identities=21% Similarity=0.636 Sum_probs=20.1
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
..+|.+|++-+. ++.....+.|+.||..
T Consensus 3 ~y~C~~CG~~~~----~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVE----LDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEE----ECCCCCceECCCCCCe
Confidence 468999999632 3334336999999984
No 10
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.50 E-value=0.45 Score=28.22 Aligned_cols=31 Identities=23% Similarity=0.561 Sum_probs=19.6
Q ss_pred ceecCCCCeEEc-CceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRN-PFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiN-p~~~~~~~g~~w~C~~C~~ 118 (187)
.++|.+|++-.+ +-.++...|.+.+|.-|++
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 467777777644 3333445567777777775
No 11
>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=80.47 E-value=0.85 Score=27.74 Aligned_cols=30 Identities=20% Similarity=0.415 Sum_probs=23.8
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
-||.+|+....-+..+.. .....|+-||..
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGST 35 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCCC
Confidence 589999988777776665 567999999983
No 12
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=79.28 E-value=1.1 Score=27.97 Aligned_cols=27 Identities=30% Similarity=0.579 Sum_probs=18.5
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-|.+|+..+-+-- ..++..|+|.-|+.
T Consensus 2 FCp~Cg~~l~~~~--~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKE--GKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCcccccc--CCCCCEEECCcCCC
Confidence 4889999763331 12234899999997
No 13
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=78.79 E-value=1.4 Score=25.35 Aligned_cols=24 Identities=25% Similarity=0.559 Sum_probs=16.0
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
+|..||=...+- ..-|.|++|+..
T Consensus 3 ~C~~CGy~y~~~------~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGE------EAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCC------cCCCcCcCCCCc
Confidence 678887443332 246999999874
No 14
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.83 E-value=0.85 Score=30.14 Aligned_cols=12 Identities=50% Similarity=1.115 Sum_probs=5.6
Q ss_pred CCCCceecCCCC
Q 029839 84 GESGLVRCCCCR 95 (187)
Q Consensus 84 ~~~~~~RC~~C~ 95 (187)
|+..|.||.+||
T Consensus 34 Ge~~I~Rc~~CR 45 (61)
T COG2888 34 GEVEIYRCAKCR 45 (61)
T ss_pred CceeeehhhhHH
Confidence 334445555444
No 15
>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=76.51 E-value=2.5 Score=25.61 Aligned_cols=26 Identities=31% Similarity=0.669 Sum_probs=19.8
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+|.+|++- ...++.....++|..||.
T Consensus 2 ~Cp~Cg~~---~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSK---EIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSS---EEEEETTTTEEEETTT-B
T ss_pred CCcCCcCC---ceEEcCCCCeEECCCCCC
Confidence 69999984 245677777899999997
No 16
>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=75.52 E-value=1.8 Score=32.20 Aligned_cols=32 Identities=13% Similarity=0.249 Sum_probs=26.6
Q ss_pred CceecCCCCeEEcCceEEEe-CCceEEEecCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVD-NGKSFVCNFCGL 118 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~-~g~~w~C~~C~~ 118 (187)
....|..|+-.+..-|.... ....|.|++|..
T Consensus 70 ~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 70 RGRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp TCEEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred CCCcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 34889999999999998874 467899999976
No 17
>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=74.64 E-value=2 Score=31.92 Aligned_cols=30 Identities=13% Similarity=0.063 Sum_probs=21.2
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCCCc
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGR 121 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~~ 121 (187)
..-.||.+|+... ......|.|+.||..+.
T Consensus 68 p~~~~C~~Cg~~~------~~~~~~~~CP~Cgs~~~ 97 (115)
T TIGR00100 68 PVECECEDCSEEV------SPEIDLYRCPKCHGIML 97 (115)
T ss_pred CcEEEcccCCCEE------ecCCcCccCcCCcCCCc
Confidence 3468999999653 33334589999998543
No 18
>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=74.55 E-value=1.6 Score=25.76 Aligned_cols=29 Identities=24% Similarity=0.396 Sum_probs=20.2
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.||..|+....-...... +....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 489999987555444332 55688999987
No 19
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=74.27 E-value=2 Score=31.82 Aligned_cols=29 Identities=14% Similarity=0.279 Sum_probs=20.8
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~ 120 (187)
..-.||..|+.. |......|.|+-||..+
T Consensus 68 p~~~~C~~Cg~~------~~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 68 PAQAWCWDCSQV------VEIHQHDAQCPHCHGER 96 (113)
T ss_pred CcEEEcccCCCE------EecCCcCccCcCCCCCC
Confidence 356899999955 33334567899999843
No 20
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=74.10 E-value=3.5 Score=27.96 Aligned_cols=25 Identities=32% Similarity=0.840 Sum_probs=17.4
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+.|| +||.|+ | -.++.+.-+| .||.
T Consensus 3 ifrC-~Cgr~l--y--a~e~~kTkkC-~CG~ 27 (68)
T PF09082_consen 3 IFRC-DCGRYL--Y--AKEGAKTKKC-VCGK 27 (68)
T ss_dssp EEEE-TTS--E--E--EETT-SEEEE-TTTE
T ss_pred EEEe-cCCCEE--E--ecCCcceeEe-cCCC
Confidence 6899 799984 3 3567788899 9998
No 21
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=74.05 E-value=1.4 Score=28.11 Aligned_cols=30 Identities=30% Similarity=0.666 Sum_probs=19.3
Q ss_pred ecCCCCeEEcCc-----------eEEEeCCceEEEecCCCC
Q 029839 90 RCCCCRGYRNPF-----------MEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 90 RC~~C~ayiNp~-----------~~~~~~g~~w~C~~C~~~ 119 (187)
+|..|+=..+|- +.|..--..|+|+.|+..
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 677777666643 234344456999999873
No 22
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.37 E-value=2.2 Score=25.08 Aligned_cols=30 Identities=20% Similarity=0.513 Sum_probs=17.3
Q ss_pred eecCCCCeEEc-CceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRN-PFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiN-p~~~~~~~g~~w~C~~C~~ 118 (187)
++|.+|++-.+ +=-++-..|.+.+|.-|++
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 56777776533 2222334566777777765
No 23
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=71.43 E-value=2.5 Score=31.29 Aligned_cols=30 Identities=20% Similarity=0.269 Sum_probs=20.4
Q ss_pred CCceecCCCCeEEcCceEEEeCCc-eEEEecCCCCCc
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGK-SFVCNFCGLDGR 121 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~-~w~C~~C~~~~~ 121 (187)
..-.||.+|+.+ |..... .|.|+.||....
T Consensus 68 p~~~~C~~Cg~~------~~~~~~~~~~CP~Cgs~~~ 98 (114)
T PRK03681 68 EAECWCETCQQY------VTLLTQRVRRCPQCHGDML 98 (114)
T ss_pred CcEEEcccCCCe------eecCCccCCcCcCcCCCCc
Confidence 346899999975 322222 388999998543
No 24
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=71.19 E-value=2.3 Score=27.12 Aligned_cols=31 Identities=29% Similarity=0.608 Sum_probs=26.0
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+.+|.+|++--.|...-...|....||.|+.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl 33 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGL 33 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccH
Confidence 5789999998888776666677799999998
No 25
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=70.55 E-value=1.2 Score=26.05 Aligned_cols=28 Identities=29% Similarity=0.597 Sum_probs=12.7
Q ss_pred cCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 91 C~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
|+.|++-+.--.--.++..+++|.-|+.
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cccccChhhhhcCCCCCccceECCCCCC
Confidence 7778776543332224556788888874
No 26
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=69.94 E-value=7 Score=22.61 Aligned_cols=28 Identities=32% Similarity=0.660 Sum_probs=19.0
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.+.+|..|++-. -+.......+|.+|+.
T Consensus 2 ~~~~C~~C~~~~----i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 2 NLKKCSKCGGNG----IVNKEDDYEVCIFCGS 29 (33)
T ss_pred CceEcCCCCCCe----EEEecCCeEEcccCCc
Confidence 367899998864 2323444689999986
No 27
>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=69.77 E-value=2.2 Score=26.67 Aligned_cols=30 Identities=23% Similarity=0.490 Sum_probs=21.0
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
-||.+|+....-+..+.. .....|+.||..
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGGE 35 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCCC
Confidence 589999986555544433 345789999984
No 28
>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=69.40 E-value=3.4 Score=24.38 Aligned_cols=26 Identities=27% Similarity=0.677 Sum_probs=19.0
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
..+|..|++. +... .+| .|+|.-||+
T Consensus 8 ~~~C~~C~~~---~~~~-~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYS-DDG-FYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCe---EeEc-cCC-EEEhhhCce
Confidence 4569999999 4433 344 699999987
No 29
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=69.37 E-value=7.2 Score=36.65 Aligned_cols=38 Identities=26% Similarity=0.392 Sum_probs=29.4
Q ss_pred CCCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCC
Q 029839 148 NVMPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPV 186 (187)
Q Consensus 148 ~~~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~~lP~ 186 (187)
...|..++||||+|.. +.-+-++.++++|..+|+.|++
T Consensus 268 ~~~p~~vvfvlD~SgS-M~g~~i~~ak~al~~~l~~L~~ 305 (596)
T TIGR03788 268 QVLPRELVFVIDTSGS-MAGESIEQAKSALLLALDQLRP 305 (596)
T ss_pred cCCCceEEEEEECCCC-CCCccHHHHHHHHHHHHHhCCC
Confidence 3456679999999884 3334478899999999999875
No 30
>PRK03954 ribonuclease P protein component 4; Validated
Probab=68.79 E-value=4.1 Score=30.74 Aligned_cols=31 Identities=19% Similarity=0.391 Sum_probs=20.5
Q ss_pred eecCCCCeEEcCc----eEEEeCC---ceEEEecCCCC
Q 029839 89 VRCCCCRGYRNPF----MEFVDNG---KSFVCNFCGLD 119 (187)
Q Consensus 89 ~RC~~C~ayiNp~----~~~~~~g---~~w~C~~C~~~ 119 (187)
--|++|.+||=|- +.+..++ -.++|..||+.
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~ 102 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHI 102 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCE
Confidence 4599999999763 3333222 22489999983
No 31
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=67.63 E-value=2 Score=22.79 Aligned_cols=13 Identities=15% Similarity=0.148 Sum_probs=7.5
Q ss_pred ecCCCCeEEcCce
Q 029839 90 RCCCCRGYRNPFM 102 (187)
Q Consensus 90 RC~~C~ayiNp~~ 102 (187)
+|.+|++-+..-.
T Consensus 1 ~Cp~CG~~~~~~~ 13 (23)
T PF13240_consen 1 YCPNCGAEIEDDA 13 (23)
T ss_pred CCcccCCCCCCcC
Confidence 4677776654433
No 32
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=66.39 E-value=4.1 Score=33.00 Aligned_cols=29 Identities=28% Similarity=0.613 Sum_probs=22.7
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCCCCcc
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGRC 122 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~~~ 122 (187)
-.||++|++-|= ..+.+.+|+-|+....|
T Consensus 149 ~A~CsrC~~~L~------~~~~~l~Cp~Cg~tEkR 177 (188)
T COG1096 149 YARCSRCRAPLV------KKGNMLKCPNCGNTEKR 177 (188)
T ss_pred EEEccCCCcceE------EcCcEEECCCCCCEEee
Confidence 479999999742 26788999999995444
No 33
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=66.20 E-value=3.1 Score=26.40 Aligned_cols=24 Identities=21% Similarity=0.640 Sum_probs=17.5
Q ss_pred eecCCCCe-EEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~a-yiNp~~~~~~~g~~w~C~~C~~ 118 (187)
..|.+|++ ++-+.- ..|.|.-|+.
T Consensus 21 ~fCP~Cg~~~m~~~~------~r~~C~~Cgy 45 (50)
T PRK00432 21 KFCPRCGSGFMAEHL------DRWHCGKCGY 45 (50)
T ss_pred CcCcCCCcchheccC------CcEECCCcCC
Confidence 47999998 544332 4699999986
No 34
>PRK12722 transcriptional activator FlhC; Provisional
Probab=65.44 E-value=2.8 Score=33.98 Aligned_cols=30 Identities=37% Similarity=0.781 Sum_probs=21.3
Q ss_pred CCceecCCCCe-EEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~a-yiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-...+|+.|++ ||-.. .+....++|++|+-
T Consensus 132 L~l~~C~~Cgg~fv~~~---~e~~~~f~CplC~~ 162 (187)
T PRK12722 132 LQLSSCNCCGGHFVTHA---HDPVGSFVCGLCQP 162 (187)
T ss_pred EeeccCCCCCCCeeccc---cccCCCCcCCCCCC
Confidence 45788999998 44221 23456799999998
No 35
>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=65.20 E-value=7.7 Score=23.78 Aligned_cols=27 Identities=15% Similarity=0.461 Sum_probs=19.1
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+.|.+|++- . +..+ .....|.|.-|++
T Consensus 19 ~~CP~Cg~~-~-~~~~-~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-K-HYRL-KTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-e-eEEe-CCCCeEECCCCCC
Confidence 669999987 2 2223 3356799999985
No 36
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=65.20 E-value=3.6 Score=26.13 Aligned_cols=27 Identities=22% Similarity=0.625 Sum_probs=19.6
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.=+|.+|++-+ ..+.......|+-||+
T Consensus 6 ~Y~C~~Cg~~~----~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREV----ELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCee----ehhhccCceeCCCCCc
Confidence 45788888876 4444566688888888
No 37
>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=64.10 E-value=5.2 Score=22.86 Aligned_cols=26 Identities=27% Similarity=0.594 Sum_probs=18.0
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+.|..|++.+- +-.+..+++|.+|..
T Consensus 2 ~~C~~C~t~L~----yP~gA~~vrCs~C~~ 27 (31)
T TIGR01053 2 VVCGGCRTLLM----YPRGASSVRCALCQT 27 (31)
T ss_pred cCcCCCCcEee----cCCCCCeEECCCCCe
Confidence 46888887653 235667788888875
No 38
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=63.63 E-value=3.6 Score=31.77 Aligned_cols=27 Identities=30% Similarity=0.621 Sum_probs=20.0
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+--|.+|++-+. ...+.-+|+||+|..
T Consensus 89 ~r~CARCGGrv~----lrsNKv~wvcnlc~k 115 (169)
T KOG3799|consen 89 TRFCARCGGRVS----LRSNKVMWVCNLCRK 115 (169)
T ss_pred hhHHHhcCCeee----eccCceEEeccCCcH
Confidence 555778888754 334667899999997
No 39
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=63.41 E-value=5.6 Score=21.48 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=15.9
Q ss_pred cCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 91 C~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
|.+|+.-|-|.-+ +..|.|+-||.
T Consensus 1 C~sC~~~i~~r~~----~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQ----AVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCccc----CceEeCCCCCC
Confidence 6677777666542 55688888873
No 40
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=62.33 E-value=6.5 Score=25.32 Aligned_cols=33 Identities=15% Similarity=0.282 Sum_probs=22.0
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
..++-|++|+.-=.-+-+-+...-+|+|..|+.
T Consensus 20 r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 20 RYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred ceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 447779999875332213344455899999996
No 41
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=62.32 E-value=1.8 Score=27.21 Aligned_cols=11 Identities=36% Similarity=1.029 Sum_probs=5.6
Q ss_pred CceEEEecCCC
Q 029839 108 GKSFVCNFCGL 118 (187)
Q Consensus 108 g~~w~C~~C~~ 118 (187)
-..|+|+.|+.
T Consensus 32 p~~w~CP~C~a 42 (47)
T PF00301_consen 32 PDDWVCPVCGA 42 (47)
T ss_dssp -TT-B-TTTSS
T ss_pred CCCCcCcCCCC
Confidence 34588888876
No 42
>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=62.29 E-value=5.2 Score=26.37 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=22.6
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
.--.|..|+...-- ...++.|.|.-||..
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCCE
Confidence 35679999988655 456788999999983
No 43
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.09 E-value=3.4 Score=30.78 Aligned_cols=30 Identities=20% Similarity=0.358 Sum_probs=19.5
Q ss_pred CCceecCCCCeEEcCceEEEeCCceE-EEecCCCCCc
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSF-VCNFCGLDGR 121 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w-~C~~C~~~~~ 121 (187)
....||.+|+.+. ......+ .|+-||....
T Consensus 69 p~~~~C~~Cg~~~------~~~~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 69 KVELECKDCSHVF------KPNALDYGVCEKCHSKNV 99 (117)
T ss_pred CCEEEhhhCCCcc------ccCCccCCcCcCCCCCce
Confidence 4578999999552 2222224 5999998543
No 44
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. 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, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=60.82 E-value=2.4 Score=24.86 Aligned_cols=28 Identities=36% Similarity=0.727 Sum_probs=18.9
Q ss_pred cCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 91 C~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
|.+|++==.|..+-...|....||-|+.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 7788888788887777888779999975
No 45
>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=60.51 E-value=6 Score=22.77 Aligned_cols=13 Identities=23% Similarity=0.467 Sum_probs=9.5
Q ss_pred CCCceecCCCCeE
Q 029839 85 ESGLVRCCCCRGY 97 (187)
Q Consensus 85 ~~~~~RC~~C~ay 97 (187)
..+++||..|+.-
T Consensus 14 ~~~~irC~~CG~R 26 (32)
T PF03604_consen 14 PGDPIRCPECGHR 26 (32)
T ss_dssp TSSTSSBSSSS-S
T ss_pred CCCcEECCcCCCe
Confidence 4678899999864
No 46
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=59.89 E-value=12 Score=25.33 Aligned_cols=28 Identities=25% Similarity=0.553 Sum_probs=22.9
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-++|..|+-- -+-|.......+|..||.
T Consensus 19 ~VkCpdC~N~---q~vFshast~V~C~~CG~ 46 (67)
T COG2051 19 RVKCPDCGNE---QVVFSHASTVVTCLICGT 46 (67)
T ss_pred EEECCCCCCE---EEEeccCceEEEeccccc
Confidence 4899999865 566777788899999998
No 47
>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=58.94 E-value=6.5 Score=22.86 Aligned_cols=30 Identities=23% Similarity=0.492 Sum_probs=13.7
Q ss_pred eecCCCCeEEc-CceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRN-PFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiN-p~~~~~~~g~~w~C~~C~~ 118 (187)
++|.+|++-.. +--.+...+....|+-|++
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~ 33 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGH 33 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCC
Confidence 45666666311 1111222344566666664
No 48
>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=56.49 E-value=7.1 Score=27.98 Aligned_cols=24 Identities=29% Similarity=0.719 Sum_probs=19.0
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
.|.+|++.|.|- +..++|..|+..
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCc
Confidence 599999998653 346999999984
No 49
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=56.30 E-value=9.6 Score=21.36 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=15.9
Q ss_pred ecCCCCeEEcCc-eEEEeCCce-----EEEecCCC
Q 029839 90 RCCCCRGYRNPF-MEFVDNGKS-----FVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~-~~~~~~g~~-----w~C~~C~~ 118 (187)
||.+|+-.|-+- ..+...++. |.|..|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 577787777663 223333333 35666654
No 50
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=56.00 E-value=10 Score=23.37 Aligned_cols=24 Identities=21% Similarity=0.412 Sum_probs=15.2
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+|.+|++-+..- .+....|+-||+
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCc
Confidence 677777754422 344577777777
No 51
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=55.89 E-value=15 Score=24.22 Aligned_cols=28 Identities=25% Similarity=0.510 Sum_probs=22.5
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-++|..|+.. -.-|........|..|++
T Consensus 11 ~VkCp~C~n~---q~vFsha~t~V~C~~Cg~ 38 (59)
T PRK00415 11 KVKCPDCGNE---QVVFSHASTVVRCLVCGK 38 (59)
T ss_pred EEECCCCCCe---EEEEecCCcEEECcccCC
Confidence 4899999976 444566777899999998
No 52
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.06 E-value=7.6 Score=29.61 Aligned_cols=34 Identities=18% Similarity=0.399 Sum_probs=20.9
Q ss_pred CceecCCCCeEEcCce-------------EEEe--CCceEEEecCCCCC
Q 029839 87 GLVRCCCCRGYRNPFM-------------EFVD--NGKSFVCNFCGLDG 120 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~-------------~~~~--~g~~w~C~~C~~~~ 120 (187)
...||..|+.....-- .+.+ ....+.|+-||...
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 5689999996643320 0000 03458899999854
No 53
>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=53.98 E-value=10 Score=29.12 Aligned_cols=31 Identities=26% Similarity=0.597 Sum_probs=22.3
Q ss_pred ceecCCCCeEEcCceE-----------EEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFME-----------FVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~-----------~~~~g~~w~C~~C~~ 118 (187)
.-||..|.+-+-+-.. +......|+|+-||.
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~k 132 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGK 132 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCC
Confidence 5899999996543222 233456899999998
No 54
>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=53.55 E-value=9.6 Score=20.75 Aligned_cols=23 Identities=26% Similarity=0.613 Sum_probs=11.8
Q ss_pred cCCCCeEEcCceEEEeCCceEEEecCC
Q 029839 91 CCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (187)
Q Consensus 91 C~~C~ayiNp~~~~~~~g~~w~C~~C~ 117 (187)
|.+|+..+- +-.+...++|..|.
T Consensus 1 C~~Cr~~L~----yp~GA~sVrCa~C~ 23 (25)
T PF06943_consen 1 CGGCRTLLM----YPRGAPSVRCACCH 23 (25)
T ss_pred CCCCCceEE----cCCCCCCeECCccC
Confidence 445555432 22345556666665
No 55
>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=53.49 E-value=11 Score=27.83 Aligned_cols=26 Identities=23% Similarity=0.612 Sum_probs=19.7
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.+.|.+|.+- |.. .+|..|+|+.|++
T Consensus 2 lp~CP~C~se---ytY--~dg~~~iCpeC~~ 27 (109)
T TIGR00686 2 LPPCPKCNSE---YTY--HDGTQLICPSCLY 27 (109)
T ss_pred CCcCCcCCCc---ceE--ecCCeeECccccc
Confidence 4778888864 443 3566799999999
No 56
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=52.63 E-value=6.4 Score=29.57 Aligned_cols=34 Identities=18% Similarity=0.215 Sum_probs=20.1
Q ss_pred CCceecCCCCeEEcCc-eEEEeCCceEEEecCCCCC
Q 029839 86 SGLVRCCCCRGYRNPF-MEFVDNGKSFVCNFCGLDG 120 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~-~~~~~~g~~w~C~~C~~~~ 120 (187)
..-.|| +|+.+...- ...+.-...|.|+-||...
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKR 102 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCC
Confidence 456899 999774432 1111111237899999743
No 57
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=52.09 E-value=9.4 Score=23.57 Aligned_cols=23 Identities=17% Similarity=0.417 Sum_probs=16.8
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+.|..|+.. |.. |.+|+|..|.-
T Consensus 1 I~CDgCg~~--PI~-----G~RykC~~C~d 23 (43)
T cd02342 1 IQCDGCGVL--PIT-----GPRYKSKVKED 23 (43)
T ss_pred CCCCCCCCC--ccc-----ccceEeCCCCC
Confidence 468888854 554 67799998865
No 58
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=51.98 E-value=11 Score=24.92 Aligned_cols=12 Identities=25% Similarity=1.021 Sum_probs=6.9
Q ss_pred CceEEEecCCCC
Q 029839 108 GKSFVCNFCGLD 119 (187)
Q Consensus 108 g~~w~C~~C~~~ 119 (187)
+..|+|+-||..
T Consensus 46 ~~~Y~CP~CGF~ 57 (59)
T PRK14890 46 SNPYTCPKCGFE 57 (59)
T ss_pred CCceECCCCCCc
Confidence 344667666653
No 59
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=51.76 E-value=27 Score=26.75 Aligned_cols=64 Identities=16% Similarity=0.302 Sum_probs=36.3
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCCCCc--ccCCCCCCccCCccEEEEechhhhccCCCCcEEEEEEEcc
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGR--CLDADERPELCRGTVEFAASREFMMRNVMPPVYFFLIDVS 161 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~~--~~~~~~~pEL~~~tvE~~~p~~y~~r~~~pp~~vFvID~s 161 (187)
--.||.+||.+.-| . +-.|.-|++.+. -.....+=.+..=|+-|..+..+ ....|..+.+|++-
T Consensus 28 ~g~kC~~CG~v~~P------P--r~~Cp~C~~~~~~E~vels~~G~V~t~Tv~~~~~~~~---~~~~P~viaiV~l~ 93 (140)
T COG1545 28 LGTKCKKCGRVYFP------P--RAYCPKCGSETELEWVELSGEGKVETYTVVYVKPPGF---SLEEPYVIAIVELE 93 (140)
T ss_pred EEEEcCCCCeEEcC------C--cccCCCCCCCCceEEEEeCCCeEEEEEEEEeeCCCCc---ccCCCEEEEEEEeC
Confidence 35899999998433 2 257999998642 11112222233334455555432 23477777777764
No 60
>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=51.64 E-value=8 Score=21.97 Aligned_cols=26 Identities=31% Similarity=0.778 Sum_probs=13.0
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.+.|..|++= |.- .+|..++|+-|++
T Consensus 2 ~p~Cp~C~se---~~y--~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 2 LPKCPLCGSE---YTY--EDGELLVCPECGH 27 (30)
T ss_dssp S---TTT--------E--E-SSSEEETTTTE
T ss_pred CCCCCCCCCc---cee--ccCCEEeCCcccc
Confidence 4678888874 222 4677899999985
No 61
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=51.39 E-value=9.6 Score=23.83 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=22.4
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.+.++|..|+..+..... ......|.|.-...
T Consensus 3 ~g~l~C~~CG~~m~~~~~-~~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKR-KGKYRYYRCSNRRR 34 (58)
T ss_pred CCcEEcccCCcEeEEEEC-CCCceEEEcCCCcC
Confidence 468999999998877542 23346788877654
No 62
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=51.38 E-value=2 Score=25.36 Aligned_cols=32 Identities=22% Similarity=0.430 Sum_probs=15.0
Q ss_pred CCceecCCCCeEEcCceEE---EeCCceEEEecCC
Q 029839 86 SGLVRCCCCRGYRNPFMEF---VDNGKSFVCNFCG 117 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~---~~~g~~w~C~~C~ 117 (187)
..+++|++|+-.+...|-- ...+..|.|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence 3579999999998876642 2334459998773
No 63
>PHA00626 hypothetical protein
Probab=51.12 E-value=15 Score=24.03 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=9.7
Q ss_pred CceEEEecCCC
Q 029839 108 GKSFVCNFCGL 118 (187)
Q Consensus 108 g~~w~C~~C~~ 118 (187)
.+.|+|.-||.
T Consensus 21 snrYkCkdCGY 31 (59)
T PHA00626 21 SDDYVCCDCGY 31 (59)
T ss_pred CcceEcCCCCC
Confidence 56799999998
No 64
>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=48.98 E-value=4.2 Score=29.96 Aligned_cols=29 Identities=28% Similarity=0.560 Sum_probs=17.7
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDG 120 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~ 120 (187)
..-.||..|+.-..+ ....+.|+.||+..
T Consensus 68 p~~~~C~~Cg~~~~~------~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 68 PARARCRDCGHEFEP------DEFDFSCPRCGSPD 96 (113)
T ss_dssp --EEEETTTS-EEEC------HHCCHH-SSSSSS-
T ss_pred CCcEECCCCCCEEec------CCCCCCCcCCcCCC
Confidence 346899999987443 33337799999954
No 65
>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=47.95 E-value=9.6 Score=21.07 Aligned_cols=26 Identities=19% Similarity=0.685 Sum_probs=14.2
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~ 117 (187)
.|.+|+.++-... ..+...+.|+-|.
T Consensus 3 ~C~rC~~~~~~~~--~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIG--INGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEE--ETTEEEEE-TTTC
T ss_pred cCccCCCcceEeE--ecCCCCeECcCCc
Confidence 6899999854333 2345578888885
No 66
>PRK00420 hypothetical protein; Validated
Probab=46.21 E-value=15 Score=27.34 Aligned_cols=25 Identities=32% Similarity=0.761 Sum_probs=19.3
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-.|..|++ |+.++ .+| ...|+.||.
T Consensus 24 ~~CP~Cg~---pLf~l-k~g-~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGL---PLFEL-KDG-EVVCPVHGK 48 (112)
T ss_pred CCCCCCCC---cceec-CCC-ceECCCCCC
Confidence 57888994 67766 444 599999998
No 67
>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=45.88 E-value=10 Score=18.82 Aligned_cols=8 Identities=50% Similarity=1.377 Sum_probs=5.2
Q ss_pred EEEecCCC
Q 029839 111 FVCNFCGL 118 (187)
Q Consensus 111 w~C~~C~~ 118 (187)
|.|.+|+.
T Consensus 1 ~~C~~C~~ 8 (24)
T PF13894_consen 1 FQCPICGK 8 (24)
T ss_dssp EE-SSTS-
T ss_pred CCCcCCCC
Confidence 78999987
No 68
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=45.31 E-value=7.9 Score=23.52 Aligned_cols=9 Identities=33% Similarity=1.077 Sum_probs=7.7
Q ss_pred eecCCCCeE
Q 029839 89 VRCCCCRGY 97 (187)
Q Consensus 89 ~RC~~C~ay 97 (187)
+||.+|++|
T Consensus 2 ~kC~~CG~~ 10 (40)
T PF15288_consen 2 VKCKNCGAF 10 (40)
T ss_pred ccccccccc
Confidence 589999988
No 69
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.36 E-value=20 Score=30.45 Aligned_cols=28 Identities=21% Similarity=0.386 Sum_probs=19.0
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
--|.+|++-|- ....-+...|.|+.|..
T Consensus 245 ~pCprCG~~I~--~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPIR--RVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCeeE--EEEECCCccEECcCCcC
Confidence 45888988762 22344567899998863
No 70
>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=43.81 E-value=8.9 Score=20.94 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=12.0
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+|..|++-++-- .-.|+.||+
T Consensus 2 ~CP~C~~~V~~~--------~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPES--------AKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhh--------cCcCCCCCC
Confidence 467777765322 235666665
No 71
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=43.48 E-value=27 Score=26.71 Aligned_cols=29 Identities=28% Similarity=0.665 Sum_probs=23.3
Q ss_pred ceecCCCCeEEcCceEEEeCCceE--EEecCCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGLD 119 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w--~C~~C~~~ 119 (187)
=+-|+.|+. |=..+...++.| .|..||+.
T Consensus 97 yVlC~~C~s---PdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNR---PDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCC---CCcEEEEeCCeEEEecccCCCC
Confidence 488999996 777777777765 89999984
No 72
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=43.22 E-value=4.3 Score=26.09 Aligned_cols=29 Identities=34% Similarity=0.714 Sum_probs=23.2
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.|.+|++--.|...-..++..-.||.|+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl 29 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGL 29 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHH
Confidence 38899997777776665577789999998
No 73
>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=42.72 E-value=25 Score=19.73 Aligned_cols=25 Identities=24% Similarity=0.422 Sum_probs=13.1
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-|.+|++= +....+|..-+|.-|+.
T Consensus 5 fC~~CG~~----t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAP----TKPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--B----EEE-SSSS-EEESSSS-
T ss_pred ccCcCCcc----ccCCCCcCEeECCCCcC
Confidence 47777774 34556677788888875
No 74
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=42.46 E-value=18 Score=27.69 Aligned_cols=24 Identities=29% Similarity=0.902 Sum_probs=18.6
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.-|..|++ |.++ .+|. ..|++|++
T Consensus 29 ~hCp~Cg~---PLF~--KdG~-v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGT---PLFR--KDGE-VFCPVCGY 52 (131)
T ss_pred hhCcccCC---ccee--eCCe-EECCCCCc
Confidence 45889997 5555 6675 99999996
No 75
>PRK12860 transcriptional activator FlhC; Provisional
Probab=42.14 E-value=13 Score=30.27 Aligned_cols=31 Identities=35% Similarity=0.801 Sum_probs=22.0
Q ss_pred CCCceecCCCCe-EEcCceEEEeCCceEEEecCCC
Q 029839 85 ESGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 85 ~~~~~RC~~C~a-yiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.-...+|+.|++ ||-. ..+....++|++|.-
T Consensus 131 ~L~l~~C~~Cgg~fv~~---~~e~~~~f~CplC~~ 162 (189)
T PRK12860 131 MLQLARCCRCGGKFVTH---AHDLRHNFVCGLCQP 162 (189)
T ss_pred CeeeccCCCCCCCeecc---ccccCCCCcCCCCCC
Confidence 345789999998 4422 224556799999996
No 76
>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=42.13 E-value=23 Score=21.47 Aligned_cols=24 Identities=33% Similarity=0.836 Sum_probs=16.6
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~ 117 (187)
-.|..|+ .|.++ +.+| .-.|..|+
T Consensus 18 ~~Cp~C~---~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCG---TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred CccCCCC---CeeEE-ecCC-CEECCCCC
Confidence 3577885 47776 4555 47899985
No 77
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=41.86 E-value=15 Score=23.44 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=17.5
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
..|.+|++= -|+-.. +.+|.|.-||.+
T Consensus 20 ~~CPrCG~g--vfmA~H--~dR~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGPG--VFMADH--KDRWACGKCGYT 46 (51)
T ss_pred ccCCCCCCc--chhhhc--CceeEeccccce
Confidence 579999941 233222 237999999863
No 78
>PRK12496 hypothetical protein; Provisional
Probab=41.85 E-value=11 Score=29.60 Aligned_cols=25 Identities=24% Similarity=0.610 Sum_probs=16.7
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
-||..|+.+ |+.+...=.|++||+.
T Consensus 128 ~~C~gC~~~------~~~~~~~~~C~~CG~~ 152 (164)
T PRK12496 128 KVCKGCKKK------YPEDYPDDVCEICGSP 152 (164)
T ss_pred EECCCCCcc------ccCCCCCCcCCCCCCh
Confidence 689999977 2222122379999984
No 79
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=41.78 E-value=23 Score=21.08 Aligned_cols=27 Identities=33% Similarity=0.854 Sum_probs=15.9
Q ss_pred ecCCCCeEEcCceEEEe--CCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVD--NGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~--~g~~w~C~~C~~ 118 (187)
-|..|++- --|- |++ +...|+|+-|+.
T Consensus 5 pCP~CGG~-DrFr-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGGS-DRFR-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCCc-cccc-cccCCCCcCEEeCCCCC
Confidence 36667661 1233 443 334699999975
No 80
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=41.22 E-value=10 Score=30.35 Aligned_cols=31 Identities=39% Similarity=0.757 Sum_probs=11.8
Q ss_pred CCCceecCCCCeEEcCceEEE-eCCceEEEecCCC
Q 029839 85 ESGLVRCCCCRGYRNPFMEFV-DNGKSFVCNFCGL 118 (187)
Q Consensus 85 ~~~~~RC~~C~ayiNp~~~~~-~~g~~w~C~~C~~ 118 (187)
.-...+|.+|++= |.... +..+.+.|++|+-
T Consensus 131 ~l~l~~C~~C~~~---fv~~~~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 131 MLQLAPCRRCGGH---FVTHAHDPRHSFVCPFCQP 162 (175)
T ss_dssp SEEEEE-TTT--E---EEEESS--SS----TT---
T ss_pred CccccCCCCCCCC---eECcCCCCCcCcCCCCCCC
Confidence 3457899999983 33221 2256799999996
No 81
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=40.97 E-value=14 Score=21.27 Aligned_cols=9 Identities=44% Similarity=1.287 Sum_probs=8.3
Q ss_pred eEEEecCCC
Q 029839 110 SFVCNFCGL 118 (187)
Q Consensus 110 ~w~C~~C~~ 118 (187)
.|+|..||.
T Consensus 2 ~~~C~~CG~ 10 (34)
T cd00729 2 VWVCPVCGY 10 (34)
T ss_pred eEECCCCCC
Confidence 699999998
No 82
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=40.58 E-value=14 Score=29.34 Aligned_cols=13 Identities=46% Similarity=1.165 Sum_probs=10.6
Q ss_pred CCceEEEecCCCC
Q 029839 107 NGKSFVCNFCGLD 119 (187)
Q Consensus 107 ~g~~w~C~~C~~~ 119 (187)
+|+.|+|..||..
T Consensus 131 ~~~~~vC~vCGy~ 143 (166)
T COG1592 131 EGKVWVCPVCGYT 143 (166)
T ss_pred cCCEEEcCCCCCc
Confidence 4568999999984
No 83
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.46 E-value=16 Score=30.68 Aligned_cols=25 Identities=32% Similarity=0.746 Sum_probs=19.5
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
..-..|..||. ..++.|.|.-||..
T Consensus 307 ~tS~~C~~cg~---------~~~r~~~C~~cg~~ 331 (364)
T COG0675 307 YTSKTCPCCGH---------LSGRLFKCPRCGFV 331 (364)
T ss_pred CCcccccccCC---------ccceeEECCCCCCe
Confidence 34578999998 33667999999983
No 84
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=39.79 E-value=10 Score=27.22 Aligned_cols=28 Identities=21% Similarity=0.175 Sum_probs=18.4
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.|.||++||=-.++ +.-..--.|+.|++
T Consensus 57 ~Pa~CkkCGfef~~----~~ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD----DKIKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc----cccCCcccCCcchh
Confidence 48999999855333 12233467888887
No 85
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=39.48 E-value=12 Score=25.53 Aligned_cols=31 Identities=23% Similarity=0.365 Sum_probs=16.0
Q ss_pred ceecCCCCeEEcCceE----EE-----eCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFME----FV-----DNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~----~~-----~~g~~w~C~~C~~ 118 (187)
-.-|++|++++=|-.. +. .+.-.|.|..|++
T Consensus 46 r~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 46 RTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred cccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 4579999998876533 33 2334688888874
No 86
>PRK10220 hypothetical protein; Provisional
Probab=39.35 E-value=24 Score=26.19 Aligned_cols=26 Identities=19% Similarity=0.609 Sum_probs=19.3
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.+.|..|.+- |.. .+|..|+|+-|++
T Consensus 3 lP~CP~C~se---ytY--~d~~~~vCpeC~h 28 (111)
T PRK10220 3 LPHCPKCNSE---YTY--EDNGMYICPECAH 28 (111)
T ss_pred CCcCCCCCCc---ceE--cCCCeEECCcccC
Confidence 4678888864 442 3566799999999
No 87
>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
Probab=39.02 E-value=54 Score=27.52 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=25.0
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhc
Q 029839 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISD 183 (187)
Q Consensus 150 ~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~~ 183 (187)
.|...+|+||+|..- . +.+..+++++...|+.
T Consensus 52 ~p~~vvlvlD~SgSM-~-~~~~~a~~a~~~~l~~ 83 (296)
T TIGR03436 52 LPLTVGLVIDTSGSM-R-NDLDRARAAAIRFLKT 83 (296)
T ss_pred CCceEEEEEECCCCc-h-HHHHHHHHHHHHHHHh
Confidence 588899999998753 2 3477788888888876
No 88
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 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 MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=38.96 E-value=9.2 Score=24.06 Aligned_cols=13 Identities=15% Similarity=0.588 Sum_probs=5.3
Q ss_pred eCCceEEEecCCC
Q 029839 106 DNGKSFVCNFCGL 118 (187)
Q Consensus 106 ~~g~~w~C~~C~~ 118 (187)
...+.|.|++|++
T Consensus 37 ~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 37 QRTPKWKCPICNK 49 (50)
T ss_dssp HHS---B-TTT--
T ss_pred hccCCeECcCCcC
Confidence 3456699999985
No 89
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=38.58 E-value=22 Score=21.16 Aligned_cols=11 Identities=27% Similarity=0.667 Sum_probs=5.4
Q ss_pred CceecCCCCeE
Q 029839 87 GLVRCCCCRGY 97 (187)
Q Consensus 87 ~~~RC~~C~ay 97 (187)
.+-+|.+|++.
T Consensus 18 ~id~C~~C~G~ 28 (41)
T PF13453_consen 18 EIDVCPSCGGI 28 (41)
T ss_pred EEEECCCCCeE
Confidence 34455555554
No 90
>PRK13685 hypothetical protein; Provisional
Probab=37.06 E-value=60 Score=28.00 Aligned_cols=36 Identities=33% Similarity=0.304 Sum_probs=26.9
Q ss_pred CcEEEEEEEcchhhHhh----cHHHHHHHHHHHHHhcCCC
Q 029839 151 PPVYFFLIDVSTDAVQT----GATAAACSAIMQVISDLPV 186 (187)
Q Consensus 151 pp~~vFvID~s~~~~~~----g~l~~~~~sL~~~L~~lP~ 186 (187)
+-..+||||+|.+-..+ .-++.++++++..|+.+++
T Consensus 88 ~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~ 127 (326)
T PRK13685 88 RAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTP 127 (326)
T ss_pred CceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCC
Confidence 44689999998753221 3488999999999999853
No 91
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=35.70 E-value=28 Score=22.65 Aligned_cols=25 Identities=40% Similarity=0.778 Sum_probs=19.2
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
..+..|.+||.+.=| .-+|..||..
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y 49 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYY 49 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcC
Confidence 457899999998655 4578888873
No 92
>PF12773 DZR: Double zinc ribbon
Probab=35.60 E-value=13 Score=22.79 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=20.9
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
.+-..|.+|++-+. ......++|.-|++.
T Consensus 10 ~~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP-----PPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCChh-----hccCCCCCCcCCcCC
Confidence 44678888888876 344556888888874
No 93
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=35.04 E-value=61 Score=22.84 Aligned_cols=35 Identities=14% Similarity=0.136 Sum_probs=24.8
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCCC
Q 029839 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLPV 186 (187)
Q Consensus 150 ~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~~lP~ 186 (187)
....|.|-||+... +..-++.+++.|+..|..-|.
T Consensus 53 ~~~~Y~FfVDieg~--~~~~~~~~l~~L~~~~~~~~~ 87 (90)
T cd04931 53 NKDEYEFFINLDKK--SAPALDPIIKSLRNDIGATVH 87 (90)
T ss_pred CCceEEEEEEEEcC--CCHHHHHHHHHHHHHhCCCCc
Confidence 34579999999764 234467788888887765443
No 94
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=35.02 E-value=21 Score=26.05 Aligned_cols=10 Identities=40% Similarity=1.076 Sum_probs=8.9
Q ss_pred ceEEEecCCC
Q 029839 109 KSFVCNFCGL 118 (187)
Q Consensus 109 ~~w~C~~C~~ 118 (187)
++|+|-+||.
T Consensus 1 ~kWkC~iCg~ 10 (101)
T PF09943_consen 1 KKWKCYICGK 10 (101)
T ss_pred CceEEEecCC
Confidence 3699999998
No 95
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=34.97 E-value=22 Score=26.95 Aligned_cols=31 Identities=23% Similarity=0.420 Sum_probs=22.8
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
...-+|..|+..+-.+... ...++.|..|+.
T Consensus 121 ~~~~~C~~C~~~~~r~~~~--~~~~~~C~~C~~ 151 (157)
T PF10263_consen 121 KYVYRCPSCGREYKRHRRS--KRKRYRCGRCGG 151 (157)
T ss_pred ceEEEcCCCCCEeeeeccc--chhhEECCCCCC
Confidence 4578899999877666655 455689999984
No 96
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=34.89 E-value=25 Score=21.74 Aligned_cols=23 Identities=35% Similarity=0.839 Sum_probs=16.4
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
++|..|+.. |.. |.+|+|..|.-
T Consensus 1 V~Cd~C~~~--pI~-----G~RykC~~C~d 23 (45)
T cd02344 1 VTCDGCQMF--PIN-----GPRFKCRNCDD 23 (45)
T ss_pred CCCCCCCCC--CCc-----cCeEECCCCCC
Confidence 367888754 333 67899999985
No 97
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=34.12 E-value=17 Score=34.91 Aligned_cols=25 Identities=24% Similarity=0.491 Sum_probs=19.0
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
...-+|..|+ |+ .|..|.|+.||.+
T Consensus 624 ~~~~~C~~CG-~~--------~g~~~~CP~CG~~ 648 (656)
T PRK08270 624 PTFSICPKHG-YL--------SGEHEFCPKCGEE 648 (656)
T ss_pred CCCcccCCCC-Cc--------CCCCCCCcCCcCc
Confidence 4567899999 43 3567999999963
No 98
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=33.95 E-value=16 Score=24.54 Aligned_cols=22 Identities=23% Similarity=0.493 Sum_probs=15.9
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
..-|++|+.... ++ +|+.||..
T Consensus 5 ~~AC~~C~~i~~--------~~--~Cp~Cgs~ 26 (64)
T PRK06393 5 YRACKKCKRLTP--------EK--TCPVHGDE 26 (64)
T ss_pred hhhHhhCCcccC--------CC--cCCCCCCC
Confidence 345899988762 22 89999984
No 99
>PLN00209 ribosomal protein S27; Provisional
Probab=33.40 E-value=51 Score=23.35 Aligned_cols=28 Identities=25% Similarity=0.497 Sum_probs=21.9
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-++|..|+..= .-|........|..|++
T Consensus 36 ~VkCp~C~n~q---~VFShA~t~V~C~~Cg~ 63 (86)
T PLN00209 36 DVKCQGCFNIT---TVFSHSQTVVVCGSCQT 63 (86)
T ss_pred EEECCCCCCee---EEEecCceEEEccccCC
Confidence 48999999874 34555677789999998
No 100
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=33.22 E-value=22 Score=18.24 Aligned_cols=8 Identities=38% Similarity=1.265 Sum_probs=6.8
Q ss_pred EEEecCCC
Q 029839 111 FVCNFCGL 118 (187)
Q Consensus 111 w~C~~C~~ 118 (187)
|.|.+|+.
T Consensus 1 ~~C~~C~~ 8 (25)
T PF12874_consen 1 FYCDICNK 8 (25)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 78999986
No 101
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=32.93 E-value=40 Score=28.56 Aligned_cols=27 Identities=19% Similarity=0.333 Sum_probs=18.7
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-|.+|++-|-- ...-+...|.|+.|..
T Consensus 247 pC~~Cg~~I~~--~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEK--IKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCeeEE--EEECCCCcEECcCCCC
Confidence 49999987632 2334567899999974
No 102
>PF08879 WRC: WRC; InterPro: IPR014977 WRC is named after the conserved Trp-Arg-Cys motif, it contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that WRC functions in DNA binding []. ; GO: 0005515 protein binding
Probab=32.18 E-value=21 Score=22.33 Aligned_cols=10 Identities=30% Similarity=0.846 Sum_probs=8.0
Q ss_pred eCCceEEEec
Q 029839 106 DNGKSFVCNF 115 (187)
Q Consensus 106 ~~g~~w~C~~ 115 (187)
.+|+.|.|.-
T Consensus 10 ~DGK~WrC~~ 19 (46)
T PF08879_consen 10 NDGKGWRCSR 19 (46)
T ss_pred CCCCccccCC
Confidence 5788999975
No 103
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=32.01 E-value=31 Score=21.22 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=20.3
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
..+..|..|+..|-. .....+.|..|+.
T Consensus 9 ~~~~~C~~C~~~i~g-----~~~~g~~C~~C~~ 36 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG-----LGKQGYRCSWCGL 36 (53)
T ss_dssp SSTEB-TTSSSBECS-----SSSCEEEETTTT-
T ss_pred CCCCCCcccCcccCC-----CCCCeEEECCCCC
Confidence 568899999999832 3456799999997
No 104
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=31.90 E-value=30 Score=22.25 Aligned_cols=24 Identities=38% Similarity=0.825 Sum_probs=17.6
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
..+..|..|+.+.=|+ .+|..||.
T Consensus 24 p~l~~C~~cG~~~~~H---------~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKLPH---------RVCPSCGY 47 (55)
T ss_pred CcceECCCCCCcccCe---------eECCccCe
Confidence 4578899999985444 46777776
No 105
>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=31.87 E-value=56 Score=18.91 Aligned_cols=26 Identities=23% Similarity=0.530 Sum_probs=14.5
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-|..|+..|=| +-+..++. .|.-|+.
T Consensus 3 FCp~C~nlL~p--~~~~~~~~-~C~~C~Y 28 (35)
T PF02150_consen 3 FCPECGNLLYP--KEDKEKRV-ACRTCGY 28 (35)
T ss_dssp BETTTTSBEEE--EEETTTTE-EESSSS-
T ss_pred eCCCCCccceE--cCCCccCc-CCCCCCC
Confidence 47777777644 22334443 6777765
No 106
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=31.50 E-value=28 Score=31.66 Aligned_cols=29 Identities=24% Similarity=0.422 Sum_probs=22.0
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
..-++|.+|++-+..-=+ + .|+|.-||++
T Consensus 348 ~~~p~Cp~Cg~~m~S~G~----~-g~rC~kCg~~ 376 (421)
T COG1571 348 RVNPVCPRCGGRMKSAGR----N-GFRCKKCGTR 376 (421)
T ss_pred EcCCCCCccCCchhhcCC----C-Cccccccccc
Confidence 345799999998765432 2 6999999994
No 107
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=31.43 E-value=32 Score=29.50 Aligned_cols=29 Identities=17% Similarity=0.364 Sum_probs=21.2
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
---|++|++-|---. ..+...|.|+-|..
T Consensus 245 GepC~~CGt~I~k~~--~~gR~t~~CP~CQ~ 273 (273)
T COG0266 245 GEPCRRCGTPIEKIK--LGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCccCCEeEEEE--EcCCcCEeCCCCCC
Confidence 456999999876544 34556799999974
No 108
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=31.09 E-value=24 Score=22.43 Aligned_cols=13 Identities=23% Similarity=0.409 Sum_probs=11.1
Q ss_pred CCceecCCCCeEE
Q 029839 86 SGLVRCCCCRGYR 98 (187)
Q Consensus 86 ~~~~RC~~C~ayi 98 (187)
..+++|.+|+.+|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 5799999999875
No 109
>COG2042 Uncharacterized conserved protein [Function unknown]
Probab=30.73 E-value=22 Score=28.42 Aligned_cols=46 Identities=17% Similarity=0.350 Sum_probs=32.1
Q ss_pred ceeEecCCCCCCCCeeEeeccccCCCH---HHhhhcCCceEEEEecCCCCCC
Q 029839 25 SKYIVKDTGNCSPRYIRCSLNQIPCTE---NLLKLSSMPSALMVQVLALPDP 73 (187)
Q Consensus 25 ~~~~~~d~gn~~p~~iR~T~~~~P~~~---~~~~~~~iPlgi~v~Pf~~~~~ 73 (187)
...++.+-++|+|+ +||...+-... .+...-++| |++++|+++...
T Consensus 12 ~~l~i~~~~qcDPK--kCT~~KL~R~g~a~~~r~~~~~~-~vvL~P~ae~~l 60 (179)
T COG2042 12 MKLYIYHAGQCDPK--KCTGKKLERFGLARLLRVGGKFP-GVVLTPFAEKAL 60 (179)
T ss_pred ceeEEEecCCCChh--hhhHHHHHhcchhhhhcccCccc-eeEECCCccccc
Confidence 34456788999998 77766655543 233446678 999999998643
No 110
>smart00400 ZnF_CHCC zinc finger.
Probab=30.39 E-value=72 Score=19.96 Aligned_cols=22 Identities=27% Similarity=0.560 Sum_probs=16.5
Q ss_pred CceEEEeCCceEEEecCCCCCc
Q 029839 100 PFMEFVDNGKSFVCNFCGLDGR 121 (187)
Q Consensus 100 p~~~~~~~g~~w~C~~C~~~~~ 121 (187)
|-+.+....+.|.|--|+..|.
T Consensus 13 pSf~v~~~kn~~~Cf~cg~gGd 34 (55)
T smart00400 13 PSFSVSPDKQFFHCFGCGAGGN 34 (55)
T ss_pred CCEEEECCCCEEEEeCCCCCCC
Confidence 4455666778899999998654
No 111
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=30.29 E-value=22 Score=21.99 Aligned_cols=12 Identities=33% Similarity=0.908 Sum_probs=10.3
Q ss_pred CCceecCCCCeE
Q 029839 86 SGLVRCCCCRGY 97 (187)
Q Consensus 86 ~~~~RC~~C~ay 97 (187)
.++-+|.+|++|
T Consensus 9 RGirkCp~CGt~ 20 (44)
T PF14952_consen 9 RGIRKCPKCGTY 20 (44)
T ss_pred hccccCCcCcCc
Confidence 468899999998
No 112
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=30.23 E-value=62 Score=22.88 Aligned_cols=28 Identities=21% Similarity=0.453 Sum_probs=21.8
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-++|..|+..= .-|........|..|++
T Consensus 35 ~VkCp~C~n~q---~VFShA~t~V~C~~Cg~ 62 (85)
T PTZ00083 35 DVKCPGCSQIT---TVFSHAQTVVLCGGCSS 62 (85)
T ss_pred EEECCCCCCee---EEEecCceEEEccccCC
Confidence 48999999874 34556677789999998
No 113
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.21 E-value=23 Score=32.83 Aligned_cols=30 Identities=17% Similarity=0.393 Sum_probs=14.7
Q ss_pred ceecCCCCeEE----------cCceEEEeCCceEEEecCCC
Q 029839 88 LVRCCCCRGYR----------NPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayi----------Np~~~~~~~g~~w~C~~C~~ 118 (187)
..+|.+|.+.+ ..||.+...- .|.|+-|+.
T Consensus 222 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~-~~~Cp~C~s 261 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEGKLRCHYCGYQEPI-PKTCPQCGS 261 (505)
T ss_pred ccCCCCCCCceEEecCCCeEEcCCCcCcCCC-CCCCCCCCC
Confidence 45566666443 2344433222 356666665
No 114
>PRK11827 hypothetical protein; Provisional
Probab=29.68 E-value=42 Score=22.15 Aligned_cols=28 Identities=18% Similarity=0.587 Sum_probs=21.5
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+++.|..|++=+- ++.+.+..+|..|+.
T Consensus 7 eILaCP~ckg~L~----~~~~~~~Lic~~~~l 34 (60)
T PRK11827 7 EIIACPVCNGKLW----YNQEKQELICKLDNL 34 (60)
T ss_pred hheECCCCCCcCe----EcCCCCeEECCccCe
Confidence 4889999998542 445566799999987
No 115
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=29.60 E-value=36 Score=20.65 Aligned_cols=22 Identities=36% Similarity=0.846 Sum_probs=15.4
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
+.|..|+. |. .|.+|+|..|..
T Consensus 1 v~Cd~C~~---~i-----~G~ry~C~~C~d 22 (43)
T cd02340 1 VICDGCQG---PI-----VGVRYKCLVCPD 22 (43)
T ss_pred CCCCCCCC---cC-----cCCeEECCCCCC
Confidence 36888887 22 356799999974
No 116
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=29.56 E-value=23 Score=23.51 Aligned_cols=20 Identities=25% Similarity=0.654 Sum_probs=14.6
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
-|++|+.... .+ +|+.|+..
T Consensus 5 AC~~C~~i~~--------~~--~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITT--------ED--RCPVCGSR 24 (61)
T ss_pred hhhhCCcccC--------CC--cCCCCcCC
Confidence 5889988762 21 69999983
No 117
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.11 E-value=2.7e+02 Score=27.38 Aligned_cols=81 Identities=14% Similarity=0.214 Sum_probs=46.2
Q ss_pred ceecCCCCeEEcCceEEEeCCceEEEecCCCCCcccCCCCCCccCCccEEEEech-hhhc-----cCCCCcEEEEEEEcc
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGRCLDADERPELCRGTVEFAASR-EFMM-----RNVMPPVYFFLIDVS 161 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~~~~~~~~~pEL~~~tvE~~~p~-~y~~-----r~~~pp~~vFvID~s 161 (187)
+.+|.+|.++ +.+....+.-.|-.||+... -....|+-.+...-+.-+. +... -=|..+++.|--|++
T Consensus 444 v~~Cp~Cd~~----lt~H~~~~~L~CH~Cg~~~~--~p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt 517 (730)
T COG1198 444 IAECPNCDSP----LTLHKATGQLRCHYCGYQEP--IPQSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDTT 517 (730)
T ss_pred cccCCCCCcc----eEEecCCCeeEeCCCCCCCC--CCCCCCCCCCCeeEEecccHHHHHHHHHHHCCCCcEEEEccccc
Confidence 6677777766 34555677899999999632 2456666555444444432 2111 135667766666665
Q ss_pred hhhHhhcHHHHHHHHH
Q 029839 162 TDAVQTGATAAACSAI 177 (187)
Q Consensus 162 ~~~~~~g~l~~~~~sL 177 (187)
... |.++++...+
T Consensus 518 ~~k---~~~~~~l~~~ 530 (730)
T COG1198 518 RRK---GALEDLLDQF 530 (730)
T ss_pred cch---hhHHHHHHHH
Confidence 543 4455544443
No 118
>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=28.04 E-value=41 Score=21.82 Aligned_cols=27 Identities=26% Similarity=0.614 Sum_probs=15.1
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
++|..|+..= .-|........|..|++
T Consensus 8 VkCp~C~~~q---~vFSha~t~V~C~~Cg~ 34 (55)
T PF01667_consen 8 VKCPGCYNIQ---TVFSHAQTVVKCVVCGT 34 (55)
T ss_dssp EE-TTT-SEE---EEETT-SS-EE-SSSTS
T ss_pred EECCCCCCee---EEEecCCeEEEcccCCC
Confidence 6888888763 33445566688888887
No 119
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=27.98 E-value=33 Score=28.95 Aligned_cols=19 Identities=26% Similarity=0.483 Sum_probs=15.7
Q ss_pred CceecCCCCe-EEcCceEEE
Q 029839 87 GLVRCCCCRG-YRNPFMEFV 105 (187)
Q Consensus 87 ~~~RC~~C~a-yiNp~~~~~ 105 (187)
.++||.+|++ .|+|-..|-
T Consensus 145 ~~p~C~~Cg~~~lrP~VV~f 164 (250)
T COG0846 145 LIPRCPKCGGPVLRPDVVWF 164 (250)
T ss_pred CCCcCccCCCccccCCEEEe
Confidence 4889999999 888888763
No 120
>PRK10445 endonuclease VIII; Provisional
Probab=27.87 E-value=53 Score=27.68 Aligned_cols=27 Identities=19% Similarity=0.383 Sum_probs=15.0
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~ 117 (187)
-.|.+|++-|--- ..-+...|.|+-|.
T Consensus 236 ~~Cp~Cg~~I~~~--~~~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKT--TLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEE--EECCCCcEECCCCc
Confidence 3477777665322 22345567777775
No 121
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=27.85 E-value=29 Score=26.24 Aligned_cols=29 Identities=17% Similarity=0.532 Sum_probs=19.3
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
++|--|+.. ....+....+.|.|.-|+..
T Consensus 1 v~C~fC~~~--s~~~~~~~~~~w~C~~C~q~ 29 (131)
T PF09779_consen 1 VNCWFCGQN--SKVPYDNRNSNWTCPHCEQY 29 (131)
T ss_pred CeeccCCCC--CCCCCCCCCCeeECCCCCCc
Confidence 467778776 23334444455999999994
No 122
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=27.65 E-value=45 Score=24.51 Aligned_cols=30 Identities=20% Similarity=0.281 Sum_probs=22.4
Q ss_pred eecCCCCeEEcCceE----EEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFME----FVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~----~~~~g~~w~C~~C~~ 118 (187)
--|++|.++|=|..+ +..+.=.|+|--||.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~ 90 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGT 90 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCc
Confidence 359999998666544 444446899999998
No 123
>PF14353 CpXC: CpXC protein
Probab=27.61 E-value=56 Score=24.09 Aligned_cols=11 Identities=45% Similarity=0.920 Sum_probs=8.5
Q ss_pred ceEEEecCCCC
Q 029839 109 KSFVCNFCGLD 119 (187)
Q Consensus 109 ~~w~C~~C~~~ 119 (187)
..++|+-||+.
T Consensus 37 ~~~~CP~Cg~~ 47 (128)
T PF14353_consen 37 FSFTCPSCGHK 47 (128)
T ss_pred CEEECCCCCCc
Confidence 36888888884
No 124
>PRK04351 hypothetical protein; Provisional
Probab=27.47 E-value=62 Score=25.11 Aligned_cols=31 Identities=23% Similarity=0.287 Sum_probs=21.2
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.-.-||.+|+...--.-+ .+-.++.|.-|+.
T Consensus 110 ~y~Y~C~~Cg~~~~r~Rr--~n~~~yrCg~C~g 140 (149)
T PRK04351 110 NYLYECQSCGQQYLRKRR--INTKRYRCGKCRG 140 (149)
T ss_pred eEEEECCCCCCEeeeeee--cCCCcEEeCCCCc
Confidence 357899999975432222 3456799999986
No 125
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.31 E-value=47 Score=24.09 Aligned_cols=33 Identities=21% Similarity=0.419 Sum_probs=24.1
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
.....|.+|++. .--+.++.+..+-.|..||..
T Consensus 19 pt~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 19 PKIFECPRCGKV-SISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CcEeECCCCCCe-EeeeecCCCcceEECCCCCCc
Confidence 357889999963 334445566678999999993
No 126
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=27.25 E-value=30 Score=30.81 Aligned_cols=25 Identities=20% Similarity=0.336 Sum_probs=18.5
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
...-||.+||== .-.-.|.|+-|+.
T Consensus 352 ~~~YRC~~CGF~--------a~~l~W~CPsC~~ 376 (389)
T COG2956 352 KPRYRCQNCGFT--------AHTLYWHCPSCRA 376 (389)
T ss_pred cCCceecccCCc--------ceeeeeeCCCccc
Confidence 456799999732 2344699999998
No 127
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.07 E-value=52 Score=28.01 Aligned_cols=27 Identities=15% Similarity=0.244 Sum_probs=18.0
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~ 117 (187)
--|.+|++-|-- ...-+...|.|+-|.
T Consensus 255 ~pC~~Cg~~I~~--~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIER--IKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEE--EEECCCccEECCCCc
Confidence 358888877642 233456778888886
No 128
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=26.97 E-value=42 Score=20.87 Aligned_cols=23 Identities=30% Similarity=0.696 Sum_probs=15.9
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
++|..|+.. |.. |.+|+|..|..
T Consensus 1 i~C~~C~~~--~i~-----g~R~~C~~C~d 23 (49)
T cd02338 1 VSCDGCGKS--NFT-----GRRYKCLICYD 23 (49)
T ss_pred CCCCCCcCC--CcE-----EeeEEeCCCCC
Confidence 478888842 222 56799999975
No 129
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=26.85 E-value=18 Score=32.44 Aligned_cols=56 Identities=20% Similarity=0.144 Sum_probs=34.1
Q ss_pred CCCCceecCCCCeEEcCceEEEeCCceEEEecCCCC---Cc--c----cCC-CCCCccCCccEEEEechhh
Q 029839 84 GESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD---GR--C----LDA-DERPELCRGTVEFAASREF 144 (187)
Q Consensus 84 ~~~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~---~~--~----~~~-~~~pEL~~~tvE~~~p~~y 144 (187)
|.+----|++|+.-++|--... ..|+|+ ||.. |. | .|+ ..+|. ...-|.+++|-+.
T Consensus 236 GKYh~~~c~~C~~~~~~~~~~~---~~~~Cp-CG~~i~~GV~~Rv~eLad~~~~~p~-~rppy~~~iPL~e 301 (374)
T TIGR00375 236 GKYHQTACEACGEPAVSEDAET---ACANCP-CGGRIKKGVSDRLRELSDQKLEHPV-PRPPYVHLIPLAE 301 (374)
T ss_pred CccchhhhcccCCcCCchhhhh---cCCCCC-CCCcceechHHHHHHHhcCCCCCCC-CCCCeeeeCCHHH
Confidence 4566778999998877654332 249999 9994 32 1 232 12222 2455777777654
No 130
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=26.78 E-value=50 Score=34.07 Aligned_cols=28 Identities=29% Similarity=0.714 Sum_probs=22.9
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
.---|..|+.| +..++|..|+|.-||.+
T Consensus 1189 ~g~~c~~cg~~-----~~vrngtc~~c~~cg~t 1216 (1220)
T PRK07562 1189 TGEACSECGNF-----TLVRNGTCLKCDTCGST 1216 (1220)
T ss_pred CCCcCCCcCCe-----EEEeCCeeeeccccCCC
Confidence 34459999987 56789999999999974
No 131
>PF06007 PhnJ: Phosphonate metabolism protein PhnJ; InterPro: IPR010306 This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilisation is unknown.; GO: 0042916 alkylphosphonate transport
Probab=26.74 E-value=36 Score=28.91 Aligned_cols=26 Identities=27% Similarity=0.712 Sum_probs=19.2
Q ss_pred eecCCCCe---EEcCceEEEeCCceEEEe
Q 029839 89 VRCCCCRG---YRNPFMEFVDNGKSFVCN 114 (187)
Q Consensus 89 ~RC~~C~a---yiNp~~~~~~~g~~w~C~ 114 (187)
-.|..||+ |+.-...-+.++++|+|+
T Consensus 236 ~~C~~CGs~~s~LdEvi~dd~G~~~~~CS 264 (277)
T PF06007_consen 236 GPCALCGSTDSFLDEVIDDDDGGRMFVCS 264 (277)
T ss_pred CcccccCCCceeceeeEEcCCCCEEEEEC
Confidence 37888876 666665556678899986
No 132
>COG1773 Rubredoxin [Energy production and conversion]
Probab=26.61 E-value=38 Score=22.00 Aligned_cols=11 Identities=36% Similarity=0.999 Sum_probs=7.7
Q ss_pred CceEEEecCCC
Q 029839 108 GKSFVCNFCGL 118 (187)
Q Consensus 108 g~~w~C~~C~~ 118 (187)
-..|.|+.|+.
T Consensus 34 Pd~w~CP~Cg~ 44 (55)
T COG1773 34 PDDWVCPECGV 44 (55)
T ss_pred CCccCCCCCCC
Confidence 33488888886
No 133
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=26.34 E-value=39 Score=29.03 Aligned_cols=15 Identities=33% Similarity=0.939 Sum_probs=14.3
Q ss_pred EEeCCceEEEecCCC
Q 029839 104 FVDNGKSFVCNFCGL 118 (187)
Q Consensus 104 ~~~~g~~w~C~~C~~ 118 (187)
|+.+|+.|.|+||..
T Consensus 136 w~hGGrif~CsfC~~ 150 (314)
T PF06524_consen 136 WDHGGRIFKCSFCDN 150 (314)
T ss_pred ccCCCeEEEeecCCC
Confidence 899999999999998
No 134
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.07 E-value=44 Score=24.39 Aligned_cols=31 Identities=26% Similarity=0.599 Sum_probs=17.0
Q ss_pred ceecCCCCeEEc--C----ceEEEeCCce-EEEecCCC
Q 029839 88 LVRCCCCRGYRN--P----FMEFVDNGKS-FVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiN--p----~~~~~~~g~~-w~C~~C~~ 118 (187)
|++|..|++-.. + |-....++.. |+|.-|+.
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~A 39 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDA 39 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCCCCc
Confidence 567888877432 1 1111112333 88888887
No 135
>PRK07218 replication factor A; Provisional
Probab=25.96 E-value=34 Score=31.18 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=18.6
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.-+-||+.|+=.+ .+|+|+.||.
T Consensus 295 gli~rCP~C~r~v----------~~~~C~~hG~ 317 (423)
T PRK07218 295 GLIERCPECGRVI----------QKGQCRSHGA 317 (423)
T ss_pred cceecCcCccccc----------cCCcCCCCCC
Confidence 4478999998876 2389999998
No 136
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=25.92 E-value=33 Score=20.72 Aligned_cols=26 Identities=35% Similarity=0.943 Sum_probs=12.4
Q ss_pred cCCCCeEEcCceEEEe--CCceEEEecCC
Q 029839 91 CCCCRGYRNPFMEFVD--NGKSFVCNFCG 117 (187)
Q Consensus 91 C~~C~ayiNp~~~~~~--~g~~w~C~~C~ 117 (187)
|..|++ -.-|..|++ ++..|+|+-|+
T Consensus 6 CP~CGG-~DrFri~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 6 CPICGG-KDRFRIFDDKDGRGTWICRQCG 33 (40)
T ss_dssp -TTTT--TTTEEEETT----S-EEETTTT
T ss_pred CCCCcC-ccccccCcCcccCCCEECCCCC
Confidence 666666 223333432 23469999994
No 137
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.78 E-value=58 Score=27.59 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=18.8
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
-|.+|++-|-- ...-+...|.|+-|..
T Consensus 237 pC~~Cg~~I~~--~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 237 PCPRCGTPIEK--IVVGGRGTHFCPQCQP 263 (269)
T ss_pred CCCcCCCeeEE--EEECCCCcEECCCCcC
Confidence 48889887643 2234567899999876
No 138
>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=25.54 E-value=49 Score=28.15 Aligned_cols=30 Identities=20% Similarity=0.573 Sum_probs=16.6
Q ss_pred CceecCCCCeEEcCceEEEeC-----CceEEEecCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDN-----GKSFVCNFCGL 118 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~-----g~~w~C~~C~~ 118 (187)
.-..|.=||+. |...+..+ .+...|.+|++
T Consensus 171 ~~g~CPvCGs~--P~~s~l~~~~~~G~R~L~Cs~C~t 205 (290)
T PF04216_consen 171 QRGYCPVCGSP--PVLSVLRGGEREGKRYLHCSLCGT 205 (290)
T ss_dssp T-SS-TTT-----EEEEEEE------EEEEEETTT--
T ss_pred cCCcCCCCCCc--CceEEEecCCCCccEEEEcCCCCC
Confidence 35799999998 66666444 27788999999
No 139
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=25.27 E-value=70 Score=27.58 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=22.4
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
....+|..|++ +... .+....-.+|.-||.
T Consensus 9 ~~~~~Cp~Cg~--~~iv-~d~~~Ge~vC~~CG~ 38 (310)
T PRK00423 9 EEKLVCPECGS--DKLI-YDYERGEIVCADCGL 38 (310)
T ss_pred ccCCcCcCCCC--CCee-EECCCCeEeecccCC
Confidence 45678999997 3333 455666799999998
No 140
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=24.94 E-value=37 Score=27.27 Aligned_cols=26 Identities=23% Similarity=0.531 Sum_probs=19.6
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
.--.||..|+-... .. .=.|+.||++
T Consensus 137 ~w~~rC~GC~~~f~------~~--~~~Cp~CG~~ 162 (177)
T COG1439 137 KWRLRCHGCKRIFP------EP--KDFCPICGSP 162 (177)
T ss_pred eeeEEEecCceecC------CC--CCcCCCCCCc
Confidence 34689999998855 23 3589999995
No 141
>PF06858 NOG1: Nucleolar GTP-binding protein 1 (NOG1); InterPro: IPR010674 This domain represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). The NOG1 family includes eukaryotic, bacterial and archaeal proteins. In Saccharomyces cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. In particular, NOG1 is believed to be functionally linked to ribosome biogenesis, which occurs in the nucleolus. In eukaryotes, NOG1 mutants were found to disrupt the biogenesis of the 60S ribosomal subunit []. The DRG and OBG proteins as well as the prokaryotic NOG-like proteins are homologous throughout their length to the amino half of eukaryotic NOG1, which contains the GTP binding motifs (IPR006073 from INTERPRO); the N-terminal GTP-binding motif is required for function.; GO: 0005525 GTP binding; PDB: 2E87_A.
Probab=24.50 E-value=1.4e+02 Score=19.56 Aligned_cols=32 Identities=16% Similarity=0.361 Sum_probs=17.4
Q ss_pred CCcEEEEEEEcchhh---HhhcHHHHHHHHHHHHHhc
Q 029839 150 MPPVYFFLIDVSTDA---VQTGATAAACSAIMQVISD 183 (187)
Q Consensus 150 ~pp~~vFvID~s~~~---~~~g~l~~~~~sL~~~L~~ 183 (187)
.+-+.+|++|.|... ++. --.+.+.|+..+..
T Consensus 13 L~~~ilfi~D~Se~CGysie~--Q~~L~~~ik~~F~~ 47 (58)
T PF06858_consen 13 LADAILFIIDPSEQCGYSIEE--QLSLFKEIKPLFPN 47 (58)
T ss_dssp T-SEEEEEE-TT-TTSS-HHH--HHHHHHHHHHHTTT
T ss_pred hcceEEEEEcCCCCCCCCHHH--HHHHHHHHHHHcCC
Confidence 456799999997653 221 23455666666543
No 142
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=24.33 E-value=26 Score=20.59 Aligned_cols=26 Identities=23% Similarity=0.361 Sum_probs=12.6
Q ss_pred cCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 91 C~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
|..|++.-|-... ......+|-.||.
T Consensus 4 C~~Cg~~Yh~~~~--pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 4 CPKCGRIYHIEFN--PPKVEGVCDNCGG 29 (36)
T ss_dssp ETTTTEEEETTTB----SSTTBCTTTTE
T ss_pred cCCCCCccccccC--CCCCCCccCCCCC
Confidence 6666666554332 2222345555554
No 143
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=23.72 E-value=29 Score=34.32 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=27.8
Q ss_pred CCCCceecCCCCeEEcCceEE------EeCCceEEEecCCC
Q 029839 84 GESGLVRCCCCRGYRNPFMEF------VDNGKSFVCNFCGL 118 (187)
Q Consensus 84 ~~~~~~RC~~C~ayiNp~~~~------~~~g~~w~C~~C~~ 118 (187)
......||+-|.-..+.+... ..+-+-|+||+||.
T Consensus 349 ~~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~ 389 (958)
T KOG1074|consen 349 KPFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGN 389 (958)
T ss_pred cccccchhhhhHhhcCchhhhhhhhhccCCCCCeeeccccc
Confidence 345678999999998877654 34567899999998
No 144
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=23.59 E-value=24 Score=22.88 Aligned_cols=14 Identities=36% Similarity=1.054 Sum_probs=5.4
Q ss_pred ceEEEecCCCCCcc
Q 029839 109 KSFVCNFCGLDGRC 122 (187)
Q Consensus 109 ~~w~C~~C~~~~~~ 122 (187)
+.++|++||.+|..
T Consensus 32 r~y~Cp~CgAtGd~ 45 (55)
T PF05741_consen 32 RKYVCPICGATGDN 45 (55)
T ss_dssp GG---TTT---GGG
T ss_pred hcCcCCCCcCcCcc
Confidence 45899999987654
No 145
>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....
Probab=23.52 E-value=1.6e+02 Score=22.62 Aligned_cols=29 Identities=14% Similarity=0.206 Sum_probs=20.2
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHh
Q 029839 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVIS 182 (187)
Q Consensus 150 ~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~ 182 (187)
..-..|||||.+-.. -++..++.|...|+
T Consensus 81 ~~~~iIfVvDssd~~----~l~e~~~~L~~ll~ 109 (175)
T PF00025_consen 81 NADGIIFVVDSSDPE----RLQEAKEELKELLN 109 (175)
T ss_dssp TESEEEEEEETTGGG----GHHHHHHHHHHHHT
T ss_pred ccceeEEEEecccce----eecccccchhhhcc
Confidence 346799999998543 25666777776665
No 146
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=23.43 E-value=88 Score=25.39 Aligned_cols=29 Identities=28% Similarity=0.643 Sum_probs=22.3
Q ss_pred ceecCCCCeEEcCceEEEeCCceE--EEecCCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGLD 119 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~~w--~C~~C~~~ 119 (187)
=+.|..|+. |=..+...++.| .|..||..
T Consensus 98 yV~C~~C~~---pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 98 YVICSECGL---PDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred eEECCCCCC---CCcEEEEcCCeEEEEcccCCCC
Confidence 489999996 677776655544 79999994
No 147
>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=23.06 E-value=51 Score=17.45 Aligned_cols=12 Identities=33% Similarity=1.063 Sum_probs=8.6
Q ss_pred CCceEEEecCCC
Q 029839 107 NGKSFVCNFCGL 118 (187)
Q Consensus 107 ~g~~w~C~~C~~ 118 (187)
+.+.|.|..|+.
T Consensus 11 ~~k~~~C~~C~k 22 (26)
T PF13465_consen 11 GEKPYKCPYCGK 22 (26)
T ss_dssp SSSSEEESSSSE
T ss_pred CCCCCCCCCCcC
Confidence 446688888874
No 148
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=23.03 E-value=37 Score=22.44 Aligned_cols=11 Identities=27% Similarity=0.694 Sum_probs=9.3
Q ss_pred CCceecCCCCe
Q 029839 86 SGLVRCCCCRG 96 (187)
Q Consensus 86 ~~~~RC~~C~a 96 (187)
.+.+||+.||=
T Consensus 35 ~D~irCReCG~ 45 (62)
T KOG3507|consen 35 GDVIRCRECGY 45 (62)
T ss_pred CCcEehhhcch
Confidence 67999999973
No 149
>PHA02942 putative transposase; Provisional
Probab=22.83 E-value=49 Score=29.59 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=20.6
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
.--.|+.||...- ...++.|.|.-||..
T Consensus 324 TSq~Cs~CG~~~~-----~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMV-----EIAHRYFHCPSCGYE 351 (383)
T ss_pred CCccCCCCCCccC-----cCCCCEEECCCCCCE
Confidence 4578999998642 224568999999994
No 150
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=22.74 E-value=39 Score=26.88 Aligned_cols=70 Identities=14% Similarity=0.280 Sum_probs=38.9
Q ss_pred CCHHHhhhcCC-ceEEEEecCCCCCCCCCCCceeccC---CCCceecCCCCeEEcCceEE-----------EeCCceEEE
Q 029839 49 CTENLLKLSSM-PSALMVQVLALPDPSEDPIPVVDFG---ESGLVRCCCCRGYRNPFMEF-----------VDNGKSFVC 113 (187)
Q Consensus 49 ~~~~~~~~~~i-Plgi~v~Pf~~~~~~e~~ip~v~~~---~~~~~RC~~C~ayiNp~~~~-----------~~~g~~w~C 113 (187)
.+..+.++++. +.|+.+..-.....--+-+-.++.. ...--||..|++-|-+-..= ..-...|.|
T Consensus 54 RDr~L~~r~k~g~~~i~i~~~s~~~Ql~e~~~~~~l~~~~~~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C 133 (165)
T COG1656 54 RDRELYKRAKLGIKAILIRSDSIEEQLAEFLARLGLKPRLFPEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRC 133 (165)
T ss_pred ccHHHHHHhhccCceEEEeCCCHHHHHHHHHHHhccchhcccccccCcccCCEeccCcHHHHhhccchhhhhcccceeEC
Confidence 45667777554 7788877633221000000000100 13368999999988755431 122347899
Q ss_pred ecCCC
Q 029839 114 NFCGL 118 (187)
Q Consensus 114 ~~C~~ 118 (187)
..||.
T Consensus 134 ~~Cgk 138 (165)
T COG1656 134 PKCGK 138 (165)
T ss_pred CCCcc
Confidence 99998
No 151
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=22.64 E-value=46 Score=28.33 Aligned_cols=19 Identities=26% Similarity=0.565 Sum_probs=16.7
Q ss_pred CceecCCCCeEEcCceEEE
Q 029839 87 GLVRCCCCRGYRNPFMEFV 105 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~ 105 (187)
.+++|.+|++.+-|.+.+.
T Consensus 178 ~iP~C~~Cgg~lrP~Vv~F 196 (285)
T PRK05333 178 RVPACPACGGILKPDVVFF 196 (285)
T ss_pred CCCCCCCCCCcccCCEEEc
Confidence 4789999999999999764
No 152
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized 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.
Probab=22.17 E-value=40 Score=33.92 Aligned_cols=23 Identities=22% Similarity=0.508 Sum_probs=18.6
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.+.-||.+|+.| +-+++|+.||.
T Consensus 623 v~~RKCPkCG~y----------Tlk~rCP~CG~ 645 (1095)
T TIGR00354 623 IAIRKCPQCGKE----------SFWLKCPVCGE 645 (1095)
T ss_pred EEEEECCCCCcc----------cccccCCCCCC
Confidence 457899999998 33589999997
No 153
>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=22.13 E-value=72 Score=24.01 Aligned_cols=28 Identities=32% Similarity=0.765 Sum_probs=19.8
Q ss_pred ceecCCCCeEEcCceEEEeCCc--eEEEecCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGK--SFVCNFCGL 118 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~--~w~C~~C~~ 118 (187)
=+.|..|+ ||=..+...++ .-.|..||+
T Consensus 93 yVlC~~C~---spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 93 YVLCPECG---SPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp HSSCTSTS---SSSEEEEEETTCCEEEETTTSC
T ss_pred EEEcCCCC---CCccEEEEcCCEEEEEecccCC
Confidence 48899999 45666654443 457999986
No 154
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=22.10 E-value=57 Score=26.74 Aligned_cols=15 Identities=20% Similarity=0.233 Sum_probs=6.7
Q ss_pred eecCCCCeEEcCceE
Q 029839 89 VRCCCCRGYRNPFME 103 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~ 103 (187)
++|.+|++.+-|.+.
T Consensus 137 p~C~~Cgg~lrP~vv 151 (225)
T cd01411 137 PYHAKCGGVIRPDIV 151 (225)
T ss_pred CCCCCCCCEeCCCEE
Confidence 444444444444443
No 155
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=22.10 E-value=41 Score=30.89 Aligned_cols=34 Identities=21% Similarity=0.575 Sum_probs=21.3
Q ss_pred CCceecCCCCeEEcCc-----------eEEEeCCceEEEecCCCC
Q 029839 86 SGLVRCCCCRGYRNPF-----------MEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~-----------~~~~~~g~~w~C~~C~~~ 119 (187)
...-+|..|+=.-.|- ..|+.--..|.|+.|+..
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 4456788888665554 233333345888888873
No 156
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.04 E-value=40 Score=25.51 Aligned_cols=33 Identities=18% Similarity=0.420 Sum_probs=21.2
Q ss_pred CceecCCCCeEE-cCceEEEeCCceEEEecCCCC
Q 029839 87 GLVRCCCCRGYR-NPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 87 ~~~RC~~C~ayi-Np~~~~~~~g~~w~C~~C~~~ 119 (187)
..+-|..|+++- --.-....+-++|+|.-|+.+
T Consensus 29 ~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~t 62 (129)
T COG3677 29 TKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGST 62 (129)
T ss_pred ccCcCCCCCccceeeECCccccccccccCCcCcc
Confidence 457788888885 111112233567999999994
No 157
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=21.95 E-value=62 Score=19.55 Aligned_cols=19 Identities=32% Similarity=0.917 Sum_probs=14.3
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
||..|+..- ..|+|-.|+.
T Consensus 1 ~C~~C~~~~----------~l~~CL~C~~ 19 (50)
T smart00290 1 RCSVCGTIE----------NLWLCLTCGQ 19 (50)
T ss_pred CcccCCCcC----------CeEEecCCCC
Confidence 688888642 2699999987
No 158
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=21.78 E-value=65 Score=23.77 Aligned_cols=28 Identities=32% Similarity=0.673 Sum_probs=22.0
Q ss_pred eecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 89 ~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
.-|.+|++.|=|.-. ..+..+.|.-||.
T Consensus 3 ~FCp~Cgsll~p~~~--~~~~~l~C~kCgy 30 (113)
T COG1594 3 RFCPKCGSLLYPKKD--DEGGKLVCRKCGY 30 (113)
T ss_pred cccCCccCeeEEeEc--CCCcEEECCCCCc
Confidence 459999999877663 3445899999998
No 159
>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=21.74 E-value=78 Score=26.78 Aligned_cols=26 Identities=19% Similarity=0.384 Sum_probs=17.0
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~ 117 (187)
-|.+|++-|--. ..-+...|.|+-|.
T Consensus 247 pC~~Cg~~I~~~--~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 247 PCRRCGTPIEKI--KVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCeeEEE--EECCCCCEECCCCC
Confidence 588888776432 23456678888884
No 160
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=21.30 E-value=34 Score=22.84 Aligned_cols=22 Identities=23% Similarity=0.694 Sum_probs=15.3
Q ss_pred ecCCCCeEEcCceEEEeCCceEEEecCCCC
Q 029839 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (187)
Q Consensus 90 RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~ 119 (187)
-|++|+..++. ..=+|+.||.+
T Consensus 6 AC~~Ck~l~~~--------d~e~CP~Cgs~ 27 (64)
T COG2093 6 ACKNCKRLTPE--------DTEICPVCGST 27 (64)
T ss_pred HHhhccccCCC--------CCccCCCCCCc
Confidence 48888876443 23589999984
No 162
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=21.26 E-value=1.3e+02 Score=25.67 Aligned_cols=34 Identities=21% Similarity=0.246 Sum_probs=22.5
Q ss_pred CCCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHh
Q 029839 149 VMPPVYFFLIDVSTDAVQTGATAAACSAIMQVIS 182 (187)
Q Consensus 149 ~~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~ 182 (187)
-...-+|||||.|.+---.+=+++++-++.+.|.
T Consensus 76 r~g~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~ 109 (261)
T COG1240 76 RAGNLIVFVVDASGSMAARRRMAAAKGAALSLLR 109 (261)
T ss_pred CcCCcEEEEEeCcccchhHHHHHHHHHHHHHHHH
Confidence 3456799999998753322236777777766663
No 163
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=21.17 E-value=46 Score=19.66 Aligned_cols=12 Identities=33% Similarity=1.016 Sum_probs=7.1
Q ss_pred CCceEEEecCCC
Q 029839 107 NGKSFVCNFCGL 118 (187)
Q Consensus 107 ~g~~w~C~~C~~ 118 (187)
.++.|+|+.||.
T Consensus 3 ~~~~YkC~~CGn 14 (36)
T PF06397_consen 3 KGEFYKCEHCGN 14 (36)
T ss_dssp TTEEEE-TTT--
T ss_pred cccEEEccCCCC
Confidence 356799999997
No 164
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=20.97 E-value=1.1e+02 Score=23.40 Aligned_cols=29 Identities=28% Similarity=0.756 Sum_probs=22.2
Q ss_pred ceecCCCCeEEcCceEEEeCCc--eEEEecCCCC
Q 029839 88 LVRCCCCRGYRNPFMEFVDNGK--SFVCNFCGLD 119 (187)
Q Consensus 88 ~~RC~~C~ayiNp~~~~~~~g~--~w~C~~C~~~ 119 (187)
=+.|+.|+. |=..+...++ .-.|..||+.
T Consensus 102 yVlC~~C~s---pdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGS---PDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCC---CCcEEEEcCCeEEEEcccCCCC
Confidence 589999997 6677766665 4579999984
No 165
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.91 E-value=43 Score=32.67 Aligned_cols=24 Identities=29% Similarity=0.557 Sum_probs=17.8
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
...-+|..|| |..- -.|.|+.||.
T Consensus 678 ~~~~~C~~CG-~~~~--------~~~~CP~CG~ 701 (735)
T PRK07111 678 HPVDRCPVCG-YLGV--------IEDKCPKCGS 701 (735)
T ss_pred CCCeecCCCC-CCCC--------cCccCcCCCC
Confidence 4578999999 5332 2399999996
No 166
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=20.54 E-value=59 Score=18.64 Aligned_cols=24 Identities=33% Similarity=0.555 Sum_probs=12.9
Q ss_pred CceecCCCCeEEcCceEEEeCCceEEEecCCC
Q 029839 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 87 ~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~ 118 (187)
...||.+|+.+.-| . .-.|+-|+.
T Consensus 10 ~~~rC~~Cg~~~~p------P--r~~Cp~C~s 33 (37)
T PF12172_consen 10 LGQRCRDCGRVQFP------P--RPVCPHCGS 33 (37)
T ss_dssp EEEE-TTT--EEES----------SEETTTT-
T ss_pred EEEEcCCCCCEecC------C--CcCCCCcCc
Confidence 36899999998322 2 257888875
No 167
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=20.41 E-value=1.1e+02 Score=29.20 Aligned_cols=36 Identities=17% Similarity=0.138 Sum_probs=24.9
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHhcCC
Q 029839 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVISDLP 185 (187)
Q Consensus 150 ~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~~lP 185 (187)
...-.+|+||.|.+--...+++.++..++..++.+.
T Consensus 41 ~~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~ 76 (576)
T PTZ00441 41 EEVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLN 76 (576)
T ss_pred CCceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhc
Confidence 356699999998754444555677777777776653
No 168
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.36 E-value=75 Score=30.67 Aligned_cols=30 Identities=23% Similarity=0.475 Sum_probs=18.2
Q ss_pred CceecCCCCeEE----------cCceEEEeCCceEEEecCCC
Q 029839 87 GLVRCCCCRGYR----------NPFMEFVDNGKSFVCNFCGL 118 (187)
Q Consensus 87 ~~~RC~~C~ayi----------Np~~~~~~~g~~w~C~~C~~ 118 (187)
...||.+|.+.| ..||.+.. ..|.|+-||.
T Consensus 391 ~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~--~p~~Cp~Cgs 430 (665)
T PRK14873 391 TPARCRHCTGPLGLPSAGGTPRCRWCGRAA--PDWRCPRCGS 430 (665)
T ss_pred CeeECCCCCCceeEecCCCeeECCCCcCCC--cCccCCCCcC
Confidence 367777777543 34454432 3577888877
No 169
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=20.23 E-value=44 Score=22.09 Aligned_cols=10 Identities=30% Similarity=0.843 Sum_probs=3.5
Q ss_pred ceecCCCCeE
Q 029839 88 LVRCCCCRGY 97 (187)
Q Consensus 88 ~~RC~~C~ay 97 (187)
-.+|.+|++|
T Consensus 48 g~KC~~C~SY 57 (61)
T PF14599_consen 48 GHKCSHCGSY 57 (61)
T ss_dssp ----TTTS--
T ss_pred hhcCCCCCCc
Confidence 5788888887
No 170
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.13 E-value=1.4e+02 Score=23.59 Aligned_cols=30 Identities=13% Similarity=0.346 Sum_probs=18.3
Q ss_pred CCcEEEEEEEcchhhHhhcHHHHHHHHHHHHHh
Q 029839 150 MPPVYFFLIDVSTDAVQTGATAAACSAIMQVIS 182 (187)
Q Consensus 150 ~pp~~vFvID~s~~~~~~g~l~~~~~sL~~~L~ 182 (187)
...-|+|++|-|.+.+ |+|+ +++.+-+.||
T Consensus 69 ATLYFvfvvD~sEsEL--~iLD-LIQvfVEtLD 98 (182)
T KOG0936|consen 69 ATLYFVFVVDSSESEL--GILD-LIQVFVETLD 98 (182)
T ss_pred eeEEEEEEEcCCcchh--HHHH-HHHHHHHHHH
Confidence 4567999999987764 5444 3344434433
No 171
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=20.09 E-value=67 Score=24.01 Aligned_cols=31 Identities=16% Similarity=0.193 Sum_probs=20.9
Q ss_pred CCceecCCCCeEEcCceEEEeCCceEEEecCCCCCcc
Q 029839 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLDGRC 122 (187)
Q Consensus 86 ~~~~RC~~C~ayiNp~~~~~~~g~~w~C~~C~~~~~~ 122 (187)
..-.+|..|+.++-+-. ..+.|+.|++...+
T Consensus 68 p~~~~C~~C~~~~~~e~------~~~~CP~C~s~~~~ 98 (115)
T COG0375 68 PAECWCLDCGQEVELEE------LDYRCPKCGSINLR 98 (115)
T ss_pred ccEEEeccCCCeecchh------heeECCCCCCCceE
Confidence 34689999977754433 23559999985443
No 172
>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=20.02 E-value=54 Score=16.26 Aligned_cols=8 Identities=38% Similarity=1.290 Sum_probs=6.1
Q ss_pred EEEecCCC
Q 029839 111 FVCNFCGL 118 (187)
Q Consensus 111 w~C~~C~~ 118 (187)
|.|..|+.
T Consensus 1 y~C~~C~~ 8 (23)
T PF00096_consen 1 YKCPICGK 8 (23)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 67888876
Done!