Query 032192
Match_columns 145
No_of_seqs 105 out of 631
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 10:50:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032192.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032192hhsearch_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 1E-41 2.2E-46 304.2 9.0 129 17-145 267-409 (1007)
2 COG5028 Vesicle coat complex C 100.0 5E-35 1.1E-39 259.1 6.5 124 19-145 133-270 (861)
3 KOG1985 Vesicle coat complex C 100.0 6.5E-34 1.4E-38 253.4 5.4 112 31-145 164-288 (887)
4 PLN00162 transport protein sec 99.9 3.8E-28 8.2E-33 220.1 9.7 102 34-142 6-116 (761)
5 PTZ00395 Sec24-related protein 99.9 2.4E-26 5.2E-31 213.1 6.9 136 4-144 622-788 (1560)
6 KOG1986 Vesicle coat complex C 99.8 1E-20 2.3E-25 167.2 3.9 104 33-143 5-117 (745)
7 COG5047 SEC23 Vesicle coat com 99.8 4.3E-19 9.3E-24 154.8 4.9 103 34-143 6-118 (755)
8 PF04810 zf-Sec23_Sec24: Sec23 99.6 1E-15 2.2E-20 91.1 2.1 32 87-118 1-32 (40)
9 PF09082 DUF1922: Domain of un 91.0 0.22 4.7E-06 32.8 2.4 26 87-118 2-27 (68)
10 PRK00398 rpoP DNA-directed RNA 89.6 0.35 7.6E-06 28.9 2.4 27 88-118 3-29 (46)
11 PF13719 zinc_ribbon_5: zinc-r 86.1 0.58 1.3E-05 26.8 1.7 31 88-118 2-33 (37)
12 smart00661 RPOL9 RNA polymeras 81.2 0.97 2.1E-05 27.1 1.4 27 90-118 2-28 (52)
13 TIGR01053 LSD1 zinc finger dom 80.4 1.6 3.4E-05 24.3 1.9 26 89-118 2-27 (31)
14 cd00350 rubredoxin_like Rubred 79.4 1.4 3.1E-05 24.5 1.6 23 90-118 3-25 (33)
15 PF09723 Zn-ribbon_8: Zinc rib 79.3 1 2.3E-05 26.4 1.0 29 89-118 6-34 (42)
16 COG1096 Predicted RNA-binding 75.1 2.5 5.4E-05 33.0 2.4 26 88-119 149-174 (188)
17 PF08271 TF_Zn_Ribbon: TFIIB z 74.8 3.4 7.4E-05 24.1 2.4 26 90-118 2-27 (43)
18 PF13717 zinc_ribbon_4: zinc-r 74.5 2.2 4.7E-05 24.3 1.4 30 89-118 3-33 (36)
19 PF02318 FYVE_2: FYVE-type zin 71.3 2.3 5.1E-05 30.3 1.3 31 88-118 71-102 (118)
20 cd00730 rubredoxin Rubredoxin; 71.1 1.7 3.8E-05 26.7 0.5 29 90-118 3-42 (50)
21 smart00834 CxxC_CXXC_SSSS Puta 70.0 2.5 5.5E-05 23.9 1.0 29 89-118 6-34 (41)
22 PRK12380 hydrogenase nickel in 69.6 3.2 6.9E-05 29.6 1.7 26 87-118 69-94 (113)
23 PF06943 zf-LSD1: LSD1 zinc fi 68.4 4.6 0.0001 21.4 1.7 23 91-117 1-23 (25)
24 PF11781 RRN7: RNA polymerase 68.3 3.9 8.5E-05 23.4 1.6 26 88-118 8-33 (36)
25 TIGR00100 hypA hydrogenase nic 67.8 3.8 8.1E-05 29.2 1.8 27 87-119 69-95 (115)
26 PF06827 zf-FPG_IleRS: Zinc fi 67.2 4.9 0.00011 21.6 1.8 26 90-117 3-28 (30)
27 TIGR02605 CxxC_CxxC_SSSS putat 66.4 3.1 6.7E-05 25.0 1.0 29 89-118 6-34 (52)
28 PRK03954 ribonuclease P protei 66.3 5.2 0.00011 29.1 2.3 30 89-118 65-101 (121)
29 PF08792 A2L_zn_ribbon: A2L zi 65.2 11 0.00025 21.0 3.1 28 87-118 2-29 (33)
30 PF12760 Zn_Tnp_IS1595: Transp 64.8 8.4 0.00018 22.8 2.6 27 89-118 19-45 (46)
31 COG1996 RPC10 DNA-directed RNA 63.4 4.4 9.6E-05 24.9 1.2 27 88-118 6-32 (49)
32 PF10058 DUF2296: Predicted in 62.1 7.5 0.00016 24.2 2.1 33 86-118 20-52 (54)
33 PF00301 Rubredoxin: Rubredoxi 62.1 1.9 4E-05 26.3 -0.6 13 106-118 30-42 (47)
34 PRK03681 hypA hydrogenase nick 62.1 5.6 0.00012 28.3 1.8 26 87-118 69-95 (114)
35 smart00132 LIM Zinc-binding do 61.3 7.8 0.00017 20.9 1.9 29 90-118 1-35 (39)
36 PF13240 zinc_ribbon_2: zinc-r 61.0 3.5 7.5E-05 21.2 0.4 21 90-118 1-21 (23)
37 PF07282 OrfB_Zn_ribbon: Putat 59.4 6.9 0.00015 24.8 1.7 28 87-118 27-54 (69)
38 PF14803 Nudix_N_2: Nudix N-te 59.0 3 6.5E-05 23.6 -0.1 28 91-118 3-30 (34)
39 smart00401 ZnF_GATA zinc finge 57.3 5.8 0.00013 24.3 1.0 31 88-118 3-33 (52)
40 PRK00432 30S ribosomal protein 56.7 6.4 0.00014 24.1 1.1 24 89-118 21-45 (50)
41 TIGR01384 TFS_arch transcripti 53.8 9.2 0.0002 26.3 1.7 23 90-118 2-24 (104)
42 PF13831 PHD_2: PHD-finger; PD 53.8 1.6 3.4E-05 25.0 -1.9 31 86-116 2-35 (36)
43 smart00659 RPOLCX RNA polymera 53.6 13 0.00029 22.1 2.1 24 90-118 4-27 (44)
44 PF13894 zf-C2H2_4: C2H2-type 52.5 7.5 0.00016 18.6 0.8 8 111-118 1-8 (24)
45 PRK12860 transcriptional activ 52.5 7.4 0.00016 30.5 1.1 31 85-118 131-162 (189)
46 PF01927 Mut7-C: Mut7-C RNAse 51.8 12 0.00027 27.5 2.2 31 88-118 91-132 (147)
47 PF04032 Rpr2: RNAse P Rpr2/Rp 51.8 6.3 0.00014 25.9 0.6 31 88-118 46-85 (85)
48 PF02150 RNA_POL_M_15KD: RNA p 51.3 20 0.00043 20.2 2.5 25 91-118 4-28 (35)
49 PRK00564 hypA hydrogenase nick 50.9 6.5 0.00014 28.1 0.6 29 86-119 69-97 (117)
50 PF03604 DNA_RNApol_7kD: DNA d 50.7 9.7 0.00021 21.2 1.1 14 85-98 14-27 (32)
51 COG2051 RPS27A Ribosomal prote 50.6 19 0.00042 23.5 2.7 28 88-118 19-46 (67)
52 TIGR02098 MJ0042_CXXC MJ0042 f 49.6 13 0.00028 20.8 1.6 9 110-118 25-33 (38)
53 PF13408 Zn_ribbon_recom: Reco 48.7 11 0.00024 22.6 1.3 32 86-118 3-34 (58)
54 PRK12722 transcriptional activ 47.6 8.7 0.00019 30.0 0.8 30 86-118 132-162 (187)
55 PF08274 PhnA_Zn_Ribbon: PhnA 47.2 11 0.00023 20.8 0.9 26 88-118 2-27 (30)
56 cd02340 ZZ_NBR1_like Zinc fing 47.1 13 0.00028 21.9 1.4 22 89-118 1-22 (43)
57 COG0266 Nei Formamidopyrimidin 46.9 19 0.00041 29.8 2.7 29 88-118 245-273 (273)
58 COG1592 Rubrerythrin [Energy p 46.8 16 0.00036 27.9 2.2 10 109-118 148-157 (166)
59 PF10571 UPF0547: Uncharacteri 46.7 8.5 0.00018 20.4 0.5 21 90-118 2-22 (26)
60 PRK00762 hypA hydrogenase nick 46.3 9.8 0.00021 27.5 0.9 31 87-118 69-100 (124)
61 cd00729 rubredoxin_SM Rubredox 45.5 12 0.00027 20.9 1.1 9 110-118 2-10 (34)
62 PRK03824 hypA hydrogenase nick 45.5 14 0.00031 27.0 1.7 32 87-118 69-115 (135)
63 COG2888 Predicted Zn-ribbon RN 45.1 6 0.00013 25.4 -0.3 13 84-96 34-46 (61)
64 PF07754 DUF1610: Domain of un 44.8 21 0.00046 18.7 1.8 23 91-117 1-23 (24)
65 PF00320 GATA: GATA zinc finge 44.7 6 0.00013 22.4 -0.4 28 91-118 1-28 (36)
66 COG1645 Uncharacterized Zn-fin 44.4 17 0.00038 26.8 1.9 24 89-118 29-52 (131)
67 PRK14810 formamidopyrimidine-D 44.4 22 0.00047 28.9 2.8 28 89-118 245-272 (272)
68 PF02891 zf-MIZ: MIZ/SP-RING z 43.8 7.5 0.00016 23.6 -0.0 14 105-118 36-49 (50)
69 TIGR00311 aIF-2beta translatio 43.7 30 0.00065 25.5 3.1 28 88-118 97-126 (133)
70 COG2023 RPR2 RNase P subunit R 43.1 18 0.00038 25.8 1.8 30 89-118 57-90 (105)
71 PRK14890 putative Zn-ribbon RN 42.8 7.6 0.00017 24.8 -0.1 25 84-118 32-56 (59)
72 PRK00415 rps27e 30S ribosomal 41.8 41 0.0009 21.4 3.1 28 88-118 11-38 (59)
73 COG0675 Transposase and inacti 41.8 16 0.00034 29.2 1.5 22 88-118 309-330 (364)
74 PF15288 zf-CCHC_6: Zinc knuck 41.0 10 0.00022 22.3 0.2 10 89-98 2-11 (40)
75 KOG3799 Rab3 effector RIM1 and 40.7 17 0.00036 27.3 1.4 27 88-118 89-115 (169)
76 PF05280 FlhC: Flagellar trans 40.5 10 0.00022 29.2 0.2 31 85-118 131-162 (175)
77 PRK01103 formamidopyrimidine/5 40.3 28 0.00062 28.2 2.8 27 90-118 247-273 (274)
78 PF12874 zf-met: Zinc-finger o 40.3 16 0.00035 18.1 0.9 8 111-118 1-8 (25)
79 PF09943 DUF2175: Uncharacteri 39.1 17 0.00036 25.7 1.1 9 110-118 2-10 (101)
80 PF09297 zf-NADH-PPase: NADH p 38.9 38 0.00083 18.3 2.4 25 90-118 5-29 (32)
81 cd02338 ZZ_PCMF_like Zinc fing 38.8 17 0.00037 21.9 1.0 22 89-118 1-23 (49)
82 TIGR00686 phnA alkylphosphonat 38.3 29 0.00064 24.8 2.3 26 88-118 2-27 (109)
83 PRK13945 formamidopyrimidine-D 37.8 31 0.00067 28.2 2.7 27 90-118 256-282 (282)
84 PRK14811 formamidopyrimidine-D 36.3 33 0.00072 27.9 2.6 27 90-118 237-263 (269)
85 KOG1074 Transcriptional repres 36.2 14 0.0003 35.2 0.4 35 84-118 349-389 (958)
86 COG1571 Predicted DNA-binding 36.1 21 0.00046 31.3 1.5 58 56-118 313-375 (421)
87 COG1594 RPB9 DNA-directed RNA 35.9 37 0.0008 24.2 2.5 27 90-118 4-30 (113)
88 PRK10445 endonuclease VIII; Pr 35.8 36 0.00079 27.5 2.8 27 89-117 236-262 (263)
89 COG3364 Zn-ribbon containing p 35.5 17 0.00036 26.0 0.6 27 88-118 2-28 (112)
90 PRK00420 hypothetical protein; 35.4 30 0.00066 24.8 2.0 25 89-118 24-48 (112)
91 smart00778 Prim_Zn_Ribbon Zinc 35.1 36 0.00079 19.5 1.9 26 91-118 6-33 (37)
92 PF01396 zf-C4_Topoisom: Topoi 34.1 41 0.00089 19.3 2.1 25 89-115 2-26 (39)
93 COG3357 Predicted transcriptio 33.8 16 0.00034 25.5 0.3 28 87-118 57-84 (97)
94 PF13453 zf-TFIIB: Transcripti 33.7 30 0.00065 19.8 1.5 13 86-98 17-29 (41)
95 PF06677 Auto_anti-p27: Sjogre 32.8 44 0.00096 19.6 2.1 23 90-117 19-41 (41)
96 PF04502 DUF572: Family of unk 32.3 44 0.00095 28.0 2.8 41 78-118 30-85 (324)
97 TIGR00577 fpg formamidopyrimid 32.2 43 0.00093 27.2 2.7 26 90-117 247-272 (272)
98 PF13465 zf-H2C2_2: Zinc-finge 32.1 32 0.00069 17.7 1.3 12 107-118 11-22 (26)
99 PHA00626 hypothetical protein 32.0 51 0.0011 21.0 2.3 11 108-118 21-31 (59)
100 PF00130 C1_1: Phorbol esters/ 31.3 35 0.00076 20.2 1.6 28 86-118 9-36 (53)
101 COG1439 Predicted nucleic acid 31.3 26 0.00056 27.2 1.2 25 86-118 137-161 (177)
102 PRK08270 anaerobic ribonucleos 31.2 25 0.00054 32.4 1.2 24 86-118 624-647 (656)
103 PF06524 NOA36: NOA36 protein; 30.1 30 0.00065 28.7 1.4 16 103-118 135-150 (314)
104 PRK06393 rpoE DNA-directed RNA 30.0 21 0.00046 23.2 0.4 21 88-118 5-25 (64)
105 PF08879 WRC: WRC; InterPro: 29.2 25 0.00055 21.2 0.6 10 106-115 10-19 (46)
106 cd00202 ZnF_GATA Zinc finger D 29.1 11 0.00023 23.4 -1.0 29 90-118 1-29 (54)
107 PF13696 zf-CCHC_2: Zinc knuck 28.9 31 0.00067 19.3 0.9 14 110-123 8-21 (32)
108 PF01155 HypA: Hydrogenase exp 28.8 15 0.00032 26.0 -0.6 27 87-119 69-95 (113)
109 PRK07218 replication factor A; 28.0 33 0.00071 30.0 1.3 23 86-118 295-317 (423)
110 PRK12496 hypothetical protein; 27.9 29 0.00063 26.2 0.9 25 89-119 128-152 (164)
111 PF09779 Ima1_N: Ima1 N-termin 27.9 43 0.00093 24.3 1.8 28 89-118 1-28 (131)
112 PF13248 zf-ribbon_3: zinc-rib 27.9 25 0.00053 18.3 0.4 22 89-118 3-24 (26)
113 TIGR00595 priA primosomal prot 27.6 27 0.00059 30.9 0.8 30 88-118 222-261 (505)
114 cd02344 ZZ_HERC2 Zinc finger, 27.5 42 0.00091 20.1 1.4 23 89-118 1-23 (45)
115 PF10263 SprT-like: SprT-like 27.4 38 0.00081 24.5 1.4 31 86-118 121-151 (157)
116 PF12773 DZR: Double zinc ribb 27.4 23 0.00051 20.8 0.3 27 87-118 11-37 (50)
117 COG1773 Rubredoxin [Energy pro 27.4 35 0.00077 21.5 1.1 15 104-118 30-44 (55)
118 PRK10220 hypothetical protein; 27.2 57 0.0012 23.4 2.2 26 88-118 3-28 (111)
119 PF14692 DUF4462: Domain of un 27.2 22 0.00047 19.4 0.1 13 41-53 5-17 (28)
120 PRK12286 rpmF 50S ribosomal pr 26.6 56 0.0012 20.5 1.9 24 86-118 25-48 (57)
121 smart00249 PHD PHD zinc finger 26.6 42 0.00091 18.4 1.3 31 86-116 12-47 (47)
122 COG0846 SIR2 NAD-dependent pro 26.0 39 0.00085 27.4 1.4 18 87-104 145-163 (250)
123 COG2956 Predicted N-acetylgluc 25.9 32 0.00069 29.6 0.9 25 86-118 352-376 (389)
124 PRK08351 DNA-directed RNA poly 25.5 31 0.00068 22.1 0.6 19 90-118 5-23 (61)
125 PF06397 Desulfoferrod_N: Desu 25.5 36 0.00077 19.5 0.8 12 107-118 3-14 (36)
126 PF06007 PhnJ: Phosphonate met 25.4 40 0.00086 27.7 1.3 27 89-115 236-265 (277)
127 PF14353 CpXC: CpXC protein 25.3 74 0.0016 22.5 2.6 9 110-118 38-46 (128)
128 TIGR01031 rpmF_bact ribosomal 25.2 53 0.0012 20.4 1.6 23 87-118 25-47 (55)
129 PF02591 DUF164: Putative zinc 25.0 39 0.00084 20.6 1.0 13 86-98 44-56 (56)
130 COG2093 DNA-directed RNA polym 24.2 30 0.00066 22.4 0.3 22 89-118 5-26 (64)
131 PRK05580 primosome assembly pr 23.9 33 0.00072 31.6 0.7 9 110-118 421-429 (679)
132 PF00569 ZZ: Zinc finger, ZZ t 23.4 61 0.0013 19.0 1.6 24 88-118 4-27 (46)
133 cd02339 ZZ_Mind_bomb Zinc fing 22.9 56 0.0012 19.4 1.3 23 89-118 1-23 (45)
134 PRK07111 anaerobic ribonucleos 22.9 44 0.00095 31.3 1.3 24 86-118 678-701 (735)
135 PF00096 zf-C2H2: Zinc finger, 22.7 49 0.0011 15.9 0.9 8 111-118 1-8 (23)
136 cd02342 ZZ_UBA_plant Zinc fing 22.7 58 0.0013 19.5 1.3 23 89-118 1-23 (43)
137 PF12172 DUF35_N: Rubredoxin-l 22.7 56 0.0012 18.1 1.3 25 86-118 9-33 (37)
138 KOG3507 DNA-directed RNA polym 22.7 38 0.00082 21.7 0.6 10 86-95 35-44 (62)
139 COG3677 Transposase and inacti 22.7 40 0.00086 24.5 0.8 33 86-118 28-61 (129)
140 COG0375 HybF Zn finger protein 22.5 58 0.0013 23.5 1.6 26 87-118 69-94 (115)
141 smart00290 ZnF_UBP Ubiquitin C 22.5 66 0.0014 18.7 1.6 19 90-118 1-19 (50)
142 PHA02942 putative transposase; 22.4 56 0.0012 28.0 1.8 27 87-118 324-350 (383)
143 PF07627 PSCyt3: Protein of un 22.4 14 0.00031 25.9 -1.6 23 87-109 68-94 (101)
144 PRK04351 hypothetical protein; 22.2 99 0.0021 23.1 2.8 31 86-118 110-140 (149)
145 PRK04016 DNA-directed RNA poly 22.2 36 0.00079 21.9 0.4 13 87-99 3-15 (62)
146 PF05191 ADK_lid: Adenylate ki 22.2 27 0.00058 19.9 -0.2 26 91-118 4-29 (36)
147 PRK14892 putative transcriptio 22.1 80 0.0017 22.1 2.2 31 87-118 20-50 (99)
148 PRK12336 translation initiatio 21.7 1.1E+02 0.0024 23.8 3.2 28 88-118 98-127 (201)
149 PF05907 DUF866: Eukaryotic pr 21.5 96 0.0021 23.4 2.7 31 88-118 30-72 (161)
150 PF01873 eIF-5_eIF-2B: Domain 21.2 90 0.002 22.6 2.4 28 88-118 93-122 (125)
151 smart00400 ZnF_CHCC zinc finge 21.2 1.3E+02 0.0027 18.1 2.7 22 99-120 12-33 (55)
152 PF00641 zf-RanBP: Zn-finger i 21.1 54 0.0012 17.3 0.9 9 110-118 4-12 (30)
153 TIGR00375 conserved hypothetic 20.9 29 0.00062 29.9 -0.3 31 84-118 236-266 (374)
154 COG1998 RPS31 Ribosomal protei 20.8 63 0.0014 20.0 1.3 26 89-118 20-45 (51)
155 PLN00032 DNA-directed RNA poly 20.8 43 0.00094 22.2 0.6 13 87-99 3-15 (71)
156 PRK11827 hypothetical protein; 20.5 88 0.0019 19.9 1.9 28 87-118 7-34 (60)
157 PRK00423 tfb transcription ini 20.4 1.1E+02 0.0023 25.3 3.0 30 86-118 9-38 (310)
158 PRK03988 translation initiatio 20.1 1.4E+02 0.003 22.1 3.2 28 88-118 102-131 (138)
No 1
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1e-41 Score=304.21 Aligned_cols=129 Identities=54% Similarity=1.163 Sum_probs=124.4
Q ss_pred CCCCCCccceeEecccCCCCCCeeEeecccccCCHHHHhhcCCceEEEEeecCCCCCCCCCCceeccCCCCeeeCCCCCc
Q 032192 17 VKPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRG 96 (145)
Q Consensus 17 ~~~pp~~~~~~~~~d~~n~~p~~iR~T~~~iP~~~~~~~~~~lPlg~~i~Pf~~~~~~~~~vp~v~~~~~~~~RC~~C~a 96 (145)
..+||++||+|++.|||||+|+|||+|+|+||.+.++++.++||||++|+|||.+.+.|+++|+|++++.+++||++|+|
T Consensus 267 ~~~PPl~TTd~~~~DqGN~sPr~mr~T~Y~iP~T~Dl~~as~iPLalvIqPfa~l~p~E~~~~vVd~g~sgPvRC~RCka 346 (1007)
T KOG1984|consen 267 AQPPPLVTTDFFIQDQGNCSPRFMRCTMYTIPCTNDLLKASQIPLALVIQPFATLTPNEAPVPVVDLGESGPVRCNRCKA 346 (1007)
T ss_pred CCCCCCcccceEEeccCCCCcchheeecccCCccHhHHHhcCCcceeEecccccCCcccCCCceecCCCCCCcchhhhhh
Confidence 34799999999999999999999999999999999999999999999999999998888999999999999999999999
Q ss_pred eEcCceEEEeCCceEEeeCCCC--------------CCccCCCCCCCccCcceEEEEecCCCC
Q 032192 97 YRNPFMEFVDNGKSFVCNFCGL--------------DGRCLDADERPELCRGTVEFAASREFM 145 (145)
Q Consensus 97 YiNp~~~~~~~g~~w~C~lC~~--------------~~~~~~~~~rPEL~~~tvE~~~p~~Y~ 145 (145)
|||||++|+++|++|+||||+. +|+|.|.+.||||..|||||+|+++||
T Consensus 347 YinPFmqF~~~gr~f~Cn~C~~~n~vp~~yf~~L~~~grr~D~~erpEL~~Gt~dfvatk~Y~ 409 (1007)
T KOG1984|consen 347 YINPFMQFIDGGRKFICNFCGSKNQVPDDYFNHLGPTGRRVDVEERPELCLGTVDFVATKDYC 409 (1007)
T ss_pred hcCcceEEecCCceEEecCCCccccCChhhcccCCCcccccccccCchhcccccceeeehhhh
Confidence 9999999999999999999998 477889999999999999999999996
No 2
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=5e-35 Score=259.12 Aligned_cols=124 Identities=39% Similarity=0.829 Sum_probs=113.3
Q ss_pred CCCCccceeEecccCCCCCCeeEeecccccCCHHHHhhcCCceEEEEeecCCCCCCCCCCceeccCCCCeeeCCCCCceE
Q 032192 19 PPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYR 98 (145)
Q Consensus 19 ~pp~~~~~~~~~d~~n~~p~~iR~T~~~iP~~~~~~~~~~lPlg~~i~Pf~~~~~~~~~vp~v~~~~~~~~RC~~C~aYi 98 (145)
.||+ ++.++..+++||+|+|+|+|+++||.+.+++++++||||++|+||.++.+++..+|+++ +..|+||++||+|+
T Consensus 133 ~ppl-tt~~~~~e~~n~~p~yvrsT~yaiP~t~dl~~~skiPfgLVI~Pf~~l~~e~~~vpl~~--d~~ivRCrrCrsYi 209 (861)
T COG5028 133 VPPL-TTNFVGSEQSNCSPKYVRSTMYAIPETNDLLKKSKIPFGLVIRPFLELYPEEDPVPLVE--DGSIVRCRRCRSYI 209 (861)
T ss_pred CCCc-ccceeeeccCCCCHHHHHHHHhhCCCchhHHHhcCCCceEEeehhhhcCccCCCCccCC--CCcchhhhhhHhhc
Confidence 4666 99999999999999999999999999999999999999999999999887777888876 34489999999999
Q ss_pred cCceEEEeCCceEEeeCCCC--------------CCccCCCCCCCccCcceEEEEecCCCC
Q 032192 99 NPFMEFVDNGKSFVCNFCGL--------------DGRCLDADERPELCRGTVEFAASREFM 145 (145)
Q Consensus 99 Np~~~~~~~g~~w~C~lC~~--------------~~~~~~~~~rPEL~~~tvE~~~p~~Y~ 145 (145)
|||.+|+.+|++|+||+|+. +..|.|.+.|+||.+++|||+||++|+
T Consensus 210 NPfv~fi~~g~kw~CNiC~~kN~vp~~~~~~~~~~~~r~d~~~r~El~~~vvdf~ap~~Y~ 270 (861)
T COG5028 210 NPFVQFIEQGRKWRCNICRSKNDVPEGFDNPSGPNDPRSDRYSRPELKSGVVDFLAPKEYS 270 (861)
T ss_pred CceEEEecCCcEEEEeeccccccCcccccCcCCCCCccccccccchhhceeeEEeccccee
Confidence 99999999999999999998 234567899999999999999999996
No 3
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.5e-34 Score=253.42 Aligned_cols=112 Identities=46% Similarity=0.883 Sum_probs=102.7
Q ss_pred ccCCCCCCeeEeecccccCCHHHHhhcCCceEEEEeecCCCCCCCCCCceeccCCCCeeeCCCCCceEcCceEEEeCCce
Q 032192 31 DTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKS 110 (145)
Q Consensus 31 d~~n~~p~~iR~T~~~iP~~~~~~~~~~lPlg~~i~Pf~~~~~~~~~vp~v~~~~~~~~RC~~C~aYiNp~~~~~~~g~~ 110 (145)
...||+|+|+|+|+++||++++++++++||||++|+||++++ +..++|++. ...|+||++||+|||||+.|++.|++
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 568999999999999999999999999999999999999876 334567665 57899999999999999999999999
Q ss_pred EEeeCCCC-------------CCccCCCCCCCccCcceEEEEecCCCC
Q 032192 111 FVCNFCGL-------------DGRCLDADERPELCRGTVEFAASREFM 145 (145)
Q Consensus 111 w~C~lC~~-------------~~~~~~~~~rPEL~~~tvE~~~p~~Y~ 145 (145)
|+||+|+. ++.+.++.+||||++++|||+||+|||
T Consensus 241 WrCNlC~~~NdvP~~f~~~~~t~~~~~~~~RpEl~~s~vE~iAP~eYm 288 (887)
T KOG1985|consen 241 WRCNLCGRVNDVPDDFDWDPLTGAYGDPYSRPELTSSVVEFIAPSEYM 288 (887)
T ss_pred eeechhhhhcCCcHHhhcCccccccCCcccCccccceeEEEecCcccc
Confidence 99999999 355789999999999999999999998
No 4
>PLN00162 transport protein sec23; Provisional
Probab=99.95 E-value=3.8e-28 Score=220.07 Aligned_cols=102 Identities=24% Similarity=0.323 Sum_probs=90.1
Q ss_pred CCCCCeeEeecccccCCHHHHhhcCCceEEEEeecCCCCCCCCCCceeccCCCCeeeCCCCCceEcCceEEEeCCceEEe
Q 032192 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFVC 113 (145)
Q Consensus 34 n~~p~~iR~T~~~iP~~~~~~~~~~lPlg~~i~Pf~~~~~~~~~vp~v~~~~~~~~RC~~C~aYiNp~~~~~~~g~~w~C 113 (145)
..+.++||+|||+||.++.++++++|||||+||||++.. ++|+++ .+|+||++|+|||||||+|+.++++|+|
T Consensus 6 ~e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~----~vp~v~---~~pvRC~~CraylNPf~~~d~~~~~W~C 78 (761)
T PLN00162 6 LEAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLP----ELPVLP---YDPLRCRTCRAVLNPYCRVDFQAKIWIC 78 (761)
T ss_pred hcccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCC----CCCcCC---CCCCccCCCcCEECCceEEecCCCEEEc
Confidence 356799999999999999999999999999999999763 388887 6799999999999999999999999999
Q ss_pred eCCCCC----Ccc---CCCCCCCcc--CcceEEEEecC
Q 032192 114 NFCGLD----GRC---LDADERPEL--CRGTVEFAASR 142 (145)
Q Consensus 114 ~lC~~~----~~~---~~~~~rPEL--~~~tvE~~~p~ 142 (145)
|||+.. ..+ .+.+.+||| +++||||++|+
T Consensus 79 ~~C~~~N~~P~~Y~~~~~~~~p~EL~p~~~TvEY~~p~ 116 (761)
T PLN00162 79 PFCFQRNHFPPHYSSISETNLPAELFPQYTTVEYTLPP 116 (761)
T ss_pred cCCCCCCCCchHhcccCccCCChhhcCCceeEEEECCC
Confidence 999992 222 245788999 99999999995
No 5
>PTZ00395 Sec24-related protein; Provisional
Probab=99.93 E-value=2.4e-26 Score=213.13 Aligned_cols=136 Identities=30% Similarity=0.515 Sum_probs=114.8
Q ss_pred CCceEEeccCCCCCCCCCCccceeEecccCCCCCCeeEeecccccCCHHHHhhcCCceEEEEeecCCCCCCCCCCceecc
Q 032192 4 SSVILYETRQGKSVKPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDF 83 (145)
Q Consensus 4 ~~~~~~~t~~~~~~~~pp~~~~~~~~~d~~n~~p~~iR~T~~~iP~~~~~~~~~~lPlg~~i~Pf~~~~~~~~~vp~v~~ 83 (145)
.....|+|+++.. ||+.+++|+++|+|||+|+|||+|||.||.+.++++.++|||||+++|||.+.+++ .||.++.
T Consensus 622 ~~~~~~~t~k~~~---pp~~~~~~~~~dtgn~dP~~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~e-~~~~~~~ 697 (1560)
T PTZ00395 622 KNLKVFETCKYIS---PPSYYQPYISIDTGKADPRFLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEGE-GIDKIDM 697 (1560)
T ss_pred ccchhhhhccCCC---CCCCCCceEEeecCCCChhhhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCCC-CCcccch
Confidence 4567899998766 79999999999999999999999999999999999999999999999999987765 4888776
Q ss_pred C--------CCCeeeCCCCCceEcCceEEEeCCceEEeeCCCCC------------------Ccc-CCCC----CCCccC
Q 032192 84 G--------ESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD------------------GRC-LDAD----ERPELC 132 (145)
Q Consensus 84 ~--------~~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~~------------------~~~-~~~~----~rPEL~ 132 (145)
. ..+|+||.+|++|+|+++.++.. +++.|+||.+. +++ .+.+ ..--|.
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 24799999999999999999866 78999999991 111 1222 223578
Q ss_pred cceEEEEecCCC
Q 032192 133 RGTVEFAASREF 144 (145)
Q Consensus 133 ~~tvE~~~p~~Y 144 (145)
+|+||+++|+.|
T Consensus 777 ~~~~~~~~~~~~ 788 (1560)
T PTZ00395 777 KGSVDIIIPPIY 788 (1560)
T ss_pred cCceeEEccchh
Confidence 999999999987
No 6
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.81 E-value=1e-20 Score=167.17 Aligned_cols=104 Identities=24% Similarity=0.356 Sum_probs=90.1
Q ss_pred CCCCCCeeEeecccccCCHHHHhhcCCceEEEEeecCCCCCCCCCCceeccCCCCeeeCCCCCceEcCceEEEeCCceEE
Q 032192 33 GNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFV 112 (145)
Q Consensus 33 ~n~~p~~iR~T~~~iP~~~~~~~~~~lPlg~~i~Pf~~~~~~~~~vp~v~~~~~~~~RC~~C~aYiNp~~~~~~~g~~w~ 112 (145)
.+...+.||+|||+||.++....++.+|++++++||++... +|.+. ++|+||++|+||+||||.++.+.+.|.
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 46788999999999999999999999999999999997542 56665 899999999999999999999999999
Q ss_pred eeCCCCC----Ccc---CCCCCCCcc--CcceEEEEecCC
Q 032192 113 CNFCGLD----GRC---LDADERPEL--CRGTVEFAASRE 143 (145)
Q Consensus 113 C~lC~~~----~~~---~~~~~rPEL--~~~tvE~~~p~~ 143 (145)
|+||... .+| .+.+..+|| ++.||||++++.
T Consensus 78 CpfC~qrN~~p~~Y~~is~~n~P~el~Pq~stvEy~l~~~ 117 (745)
T KOG1986|consen 78 CPFCNQRNPFPPHYSGISENNLPPELLPQYSTVEYTLSPG 117 (745)
T ss_pred ccccccCCCCChhhcccCccCCChhhcCCcceeEEecCCC
Confidence 9999992 233 245667788 899999998853
No 7
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=99.76 E-value=4.3e-19 Score=154.76 Aligned_cols=103 Identities=24% Similarity=0.394 Sum_probs=88.5
Q ss_pred CCCCCeeEeecccccCCHHHHhhcCCceEEEEeecCCCCCCCCCCceeccCCCCeeeCCC-CCceEcCceEEEeCCceEE
Q 032192 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC-CRGYRNPFMEFVDNGKSFV 112 (145)
Q Consensus 34 n~~p~~iR~T~~~iP~~~~~~~~~~lPlg~~i~Pf~~~~~~~~~vp~v~~~~~~~~RC~~-C~aYiNp~~~~~~~g~~w~ 112 (145)
+.+.++||+|||+||.++....++.+|++++|+||.+.+. +++.. ++|+.|.. |+||+||||.++.+++.|+
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----LTVNY---YEPVKCTAPCKAVLNPYCHIDERNQSWI 78 (755)
T ss_pred hccccceEEEEecccCCccccccccccHHHhccccccccc----cCccc---CCCceecccchhhcCcceeeccCCceEe
Confidence 5788999999999999999999999999999999997532 45443 88999999 9999999999999999999
Q ss_pred eeCCCCC----Ccc---CCCCCCCcc--CcceEEEEecCC
Q 032192 113 CNFCGLD----GRC---LDADERPEL--CRGTVEFAASRE 143 (145)
Q Consensus 113 C~lC~~~----~~~---~~~~~rPEL--~~~tvE~~~p~~ 143 (145)
|.||+.. .++ .+.+..+|| ++.||||+.++.
T Consensus 79 CpfCnqrn~lp~qy~~iS~~~LplellpqssTiey~lskp 118 (755)
T COG5047 79 CPFCNQRNTLPPQYRDISNANLPLELLPQSSTIEYTLSKP 118 (755)
T ss_pred cceecCCCCCChhhcCCCcccCCccccCCCceEEEEccCC
Confidence 9999992 223 234667799 899999998874
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=99.57 E-value=1e-15 Score=91.09 Aligned_cols=32 Identities=59% Similarity=1.324 Sum_probs=23.7
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+|+||++|+||||||++|+.++++|+|+||++
T Consensus 1 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 1 GPVRCRRCRAYLNPFCQFDDGGKTWICNFCGT 32 (40)
T ss_dssp -S-B-TTT--BS-TTSEEETTTTEEEETTT--
T ss_pred CccccCCCCCEECCcceEcCCCCEEECcCCCC
Confidence 48999999999999999999999999999998
No 9
>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=90.99 E-value=0.22 Score=32.77 Aligned_cols=26 Identities=31% Similarity=0.772 Sum_probs=19.3
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-+.|| +|+.++ |. .++.++-+| .||.
T Consensus 2 lifrC-~Cgr~l--ya--~e~~kTkkC-~CG~ 27 (68)
T PF09082_consen 2 LIFRC-DCGRYL--YA--KEGAKTKKC-VCGK 27 (68)
T ss_dssp EEEEE-TTS--E--EE--ETT-SEEEE-TTTE
T ss_pred EEEEe-cCCCEE--Ee--cCCcceeEe-cCCC
Confidence 37899 799998 66 578888999 9998
No 10
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.56 E-value=0.35 Score=28.86 Aligned_cols=27 Identities=22% Similarity=0.663 Sum_probs=19.7
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..+|.+|++-+- ++.....++|+.||.
T Consensus 3 ~y~C~~CG~~~~----~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGREVE----LDEYGTGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCEEE----ECCCCCceECCCCCC
Confidence 468999999652 233333699999998
No 11
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.06 E-value=0.58 Score=26.83 Aligned_cols=31 Identities=23% Similarity=0.561 Sum_probs=17.8
Q ss_pred eeeCCCCCceEc-CceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRN-PFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiN-p~~~~~~~g~~w~C~lC~~ 118 (145)
.++|.+|++-.+ |-.++...|++.+|.-|++
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 356777766554 3333445566667776664
No 12
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=81.18 E-value=0.97 Score=27.13 Aligned_cols=27 Identities=26% Similarity=0.535 Sum_probs=18.5
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-|..|+..+ +..-...+..|.|.-||.
T Consensus 2 FCp~Cg~~l--~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNML--IPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCcc--ccccCCCCCEEECCcCCC
Confidence 488999977 333222234799999998
No 13
>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=80.39 E-value=1.6 Score=24.30 Aligned_cols=26 Identities=27% Similarity=0.594 Sum_probs=18.6
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+.|..|++.+- .-.+.++++|.+|+.
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 46888888773 235677888888875
No 14
>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=79.36 E-value=1.4 Score=24.49 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=15.1
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+|..|+=...+- ...|.|++|+.
T Consensus 3 ~C~~CGy~y~~~------~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGE------EAPWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCC------cCCCcCcCCCC
Confidence 677777433332 24699999987
No 15
>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=79.28 E-value=1 Score=26.42 Aligned_cols=29 Identities=21% Similarity=0.430 Sum_probs=23.4
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-||.+|+....-+..+.. .....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 589999988877777666 56789999987
No 16
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=75.12 E-value=2.5 Score=33.03 Aligned_cols=26 Identities=35% Similarity=0.759 Sum_probs=21.6
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~~ 119 (145)
--||.+|++.| ...+.+.+|+-||.+
T Consensus 149 ~A~CsrC~~~L------~~~~~~l~Cp~Cg~t 174 (188)
T COG1096 149 YARCSRCRAPL------VKKGNMLKCPNCGNT 174 (188)
T ss_pred EEEccCCCcce------EEcCcEEECCCCCCE
Confidence 47999999988 236778999999983
No 17
>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=74.82 E-value=3.4 Score=24.13 Aligned_cols=26 Identities=31% Similarity=0.724 Sum_probs=19.5
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+|..|++-- ..++.....++|..||.
T Consensus 2 ~Cp~Cg~~~---~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKE---IVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSE---EEEETTTTEEEETTT-B
T ss_pred CCcCCcCCc---eEEcCCCCeEECCCCCC
Confidence 689999843 45677777899999998
No 18
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=74.49 E-value=2.2 Score=24.32 Aligned_cols=30 Identities=20% Similarity=0.513 Sum_probs=16.0
Q ss_pred eeCCCCCceEc-CceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRN-PFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiN-p~~~~~~~g~~w~C~lC~~ 118 (145)
++|.+|++-.+ +=-.+-..|.+.+|.-|++
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 56666666443 2222334555666666654
No 19
>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=71.33 E-value=2.3 Score=30.29 Aligned_cols=31 Identities=13% Similarity=0.268 Sum_probs=25.2
Q ss_pred eeeCCCCCceEcCceEEEe-CCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVD-NGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~-~g~~w~C~lC~~ 118 (145)
...|..|+-.+..-|.+.. ....|.|++|..
T Consensus 71 ~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 71 GRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQK 102 (118)
T ss_dssp CEEETTTTEEEETTSEEETSSSCCEEEHHHHH
T ss_pred CCcCCcCCccccCccCCcCCCCCCEEChhhHH
Confidence 4788888888888888764 467899999975
No 20
>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=71.13 E-value=1.7 Score=26.72 Aligned_cols=29 Identities=31% Similarity=0.687 Sum_probs=18.5
Q ss_pred eCCCCCceEcCc-----------eEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPF-----------MEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~-----------~~~~~~g~~w~C~lC~~ 118 (145)
+|..|+=..+|- ..|..--..|+|+.|+.
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 677777555542 23434445699999986
No 21
>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=69.96 E-value=2.5 Score=23.92 Aligned_cols=29 Identities=24% Similarity=0.396 Sum_probs=19.2
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.||..|+..+.-...... +....|+-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 488888886654444332 45678888886
No 22
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=69.64 E-value=3.2 Score=29.57 Aligned_cols=26 Identities=15% Similarity=0.257 Sum_probs=19.0
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
...||..|+... ......|.|+-||.
T Consensus 69 ~~~~C~~Cg~~~------~~~~~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVV------EIHQHDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEE------ecCCcCccCcCCCC
Confidence 468999999544 23334578999998
No 23
>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=68.43 E-value=4.6 Score=21.41 Aligned_cols=23 Identities=26% Similarity=0.613 Sum_probs=12.7
Q ss_pred CCCCCceEcCceEEEeCCceEEeeCCC
Q 032192 91 CCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (145)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~lC~ 117 (145)
|.+|+..+- .-.+...++|..|+
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 555666552 12355567777665
No 24
>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=68.28 E-value=3.9 Score=23.36 Aligned_cols=26 Identities=27% Similarity=0.700 Sum_probs=18.8
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..+|..|++. +.. ..+| .|.|.-||+
T Consensus 8 ~~~C~~C~~~---~~~-~~dG-~~yC~~cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGSR---WFY-SDDG-FYYCDRCGH 33 (36)
T ss_pred CCcCCCCCCe---EeE-ccCC-EEEhhhCce
Confidence 4679999999 332 2344 599999986
No 25
>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=67.83 E-value=3.8 Score=29.25 Aligned_cols=27 Identities=19% Similarity=0.261 Sum_probs=19.7
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~~ 119 (145)
...||.+|+....+ ....|.|+.||..
T Consensus 69 ~~~~C~~Cg~~~~~------~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 69 VECECEDCSEEVSP------EIDLYRCPKCHGI 95 (115)
T ss_pred cEEEcccCCCEEec------CCcCccCcCCcCC
Confidence 46899999965533 2235899999983
No 26
>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=67.19 E-value=4.9 Score=21.55 Aligned_cols=26 Identities=19% Similarity=0.685 Sum_probs=14.6
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~ 117 (145)
.|.+|+.++-... ..+...+.|.-|.
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 6899999974332 3455678898885
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=66.40 E-value=3.1 Score=25.03 Aligned_cols=29 Identities=24% Similarity=0.476 Sum_probs=20.1
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-||.+|+....-+..+.. .....|+.||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCC
Confidence 489999986555544333 34578999998
No 28
>PRK03954 ribonuclease P protein component 4; Validated
Probab=66.35 E-value=5.2 Score=29.11 Aligned_cols=30 Identities=20% Similarity=0.452 Sum_probs=20.3
Q ss_pred eeCCCCCceEcCce--EE-EeCC----ceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFM--EF-VDNG----KSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~--~~-~~~g----~~w~C~lC~~ 118 (145)
.-|++|.+|+=|-. .+ ...+ -.++|..||+
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~ 101 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGH 101 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCC
Confidence 45999999997743 22 2222 2348999998
No 29
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=65.20 E-value=11 Score=21.03 Aligned_cols=28 Identities=32% Similarity=0.704 Sum_probs=18.9
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.+.+|..|++-+ - +........|.+|+.
T Consensus 2 ~~~~C~~C~~~~--i--~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 2 NLKKCSKCGGNG--I--VNKEDDYEVCIFCGS 29 (33)
T ss_pred CceEcCCCCCCe--E--EEecCCeEEcccCCc
Confidence 367899999866 1 212334689999986
No 30
>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=64.80 E-value=8.4 Score=22.79 Aligned_cols=27 Identities=15% Similarity=0.512 Sum_probs=18.9
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+.|.+|++- ..+ . ......|+|.-|++
T Consensus 19 ~~CP~Cg~~-~~~-~-~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHY-R-LKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeE-E-eCCCCeEECCCCCC
Confidence 569999987 222 2 33356799999975
No 31
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=63.44 E-value=4.4 Score=24.93 Aligned_cols=27 Identities=22% Similarity=0.625 Sum_probs=18.7
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.=+|.+|++-+ ..+.....-.|.-||+
T Consensus 6 ~Y~C~~Cg~~~----~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREV----ELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCee----ehhhccCceeCCCCCc
Confidence 45788888877 4344555678888887
No 32
>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=62.11 E-value=7.5 Score=24.20 Aligned_cols=33 Identities=15% Similarity=0.282 Sum_probs=22.0
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-.+-|++|+.--.-+-+-+...-+|+|..|+.
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 346779999875443323344445799999986
No 33
>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=62.08 E-value=1.9 Score=26.27 Aligned_cols=13 Identities=38% Similarity=0.915 Sum_probs=6.4
Q ss_pred eCCceEEeeCCCC
Q 032192 106 DNGKSFVCNFCGL 118 (145)
Q Consensus 106 ~~g~~w~C~lC~~ 118 (145)
.--..|+|+.|+.
T Consensus 30 ~Lp~~w~CP~C~a 42 (47)
T PF00301_consen 30 DLPDDWVCPVCGA 42 (47)
T ss_dssp GS-TT-B-TTTSS
T ss_pred HCCCCCcCcCCCC
Confidence 3344588888875
No 34
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=62.08 E-value=5.6 Score=28.34 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=18.5
Q ss_pred CeeeCCCCCceEcCceEEEeCCc-eEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGK-SFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~-~w~C~lC~~ 118 (145)
...||..|+.+. ..... .|.|+.||.
T Consensus 69 ~~~~C~~Cg~~~------~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYV------TLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCee------ecCCccCCcCcCcCC
Confidence 468999999644 22222 388999998
No 35
>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=61.27 E-value=7.8 Score=20.92 Aligned_cols=29 Identities=24% Similarity=0.501 Sum_probs=14.9
Q ss_pred eCCCCCceEcCc-eEEEeCCceE-----EeeCCCC
Q 032192 90 RCCCCRGYRNPF-MEFVDNGKSF-----VCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~-~~~~~~g~~w-----~C~lC~~ 118 (145)
||.+|+-.|-+- ..+...++.| +|..|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 577777766653 2223333333 5555553
No 36
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=61.04 E-value=3.5 Score=21.22 Aligned_cols=21 Identities=24% Similarity=0.498 Sum_probs=12.0
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+|.+|++-+..-.+ .|.-||+
T Consensus 1 ~Cp~CG~~~~~~~~--------fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAK--------FCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCc--------chhhhCC
Confidence 47777776643322 3666664
No 37
>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=59.40 E-value=6.9 Score=24.78 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=22.0
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.--.|..|+...-- ...++.|.|.-||.
T Consensus 27 TSq~C~~CG~~~~~----~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK----RRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCccccccc----ccccceEEcCCCCC
Confidence 34679999987755 45677899999998
No 38
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=59.01 E-value=3 Score=23.63 Aligned_cols=28 Identities=29% Similarity=0.597 Sum_probs=10.9
Q ss_pred CCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
|..|++=+.--..-.++..+++|.-||.
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 6666665532221124455677777763
No 39
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=57.27 E-value=5.8 Score=24.33 Aligned_cols=31 Identities=29% Similarity=0.608 Sum_probs=25.9
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+.+|.+|++--.|...-...|..-.||-|+.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl 33 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGL 33 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccH
Confidence 5689999998888877666676789999998
No 40
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=56.73 E-value=6.4 Score=24.10 Aligned_cols=24 Identities=21% Similarity=0.541 Sum_probs=17.3
Q ss_pred eeCCCCCc-eEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~a-YiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-|.+|++ ++-+. ...|.|.-||.
T Consensus 21 ~fCP~Cg~~~m~~~------~~r~~C~~Cgy 45 (50)
T PRK00432 21 KFCPRCGSGFMAEH------LDRWHCGKCGY 45 (50)
T ss_pred CcCcCCCcchhecc------CCcEECCCcCC
Confidence 47999998 55332 24699999986
No 41
>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=53.81 E-value=9.2 Score=26.28 Aligned_cols=23 Identities=30% Similarity=0.712 Sum_probs=18.2
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-|.+|++.|.|- +..+.|..|+.
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~ 24 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGY 24 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCC
Confidence 489999999552 23699999998
No 42
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=53.78 E-value=1.6 Score=24.98 Aligned_cols=31 Identities=23% Similarity=0.452 Sum_probs=14.2
Q ss_pred CCeeeCCCCCceEcCceEE---EeCCceEEeeCC
Q 032192 86 SGLVRCCCCRGYRNPFMEF---VDNGKSFVCNFC 116 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~---~~~g~~w~C~lC 116 (145)
..+++|++|.-.+.-.|.- ...+..|.|..|
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C 35 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRC 35 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-----HHH
T ss_pred CceEEeCCCCCcCChhhCCcccCCCCCcEECCcC
Confidence 3579999999988854432 234445999776
No 43
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=53.55 E-value=13 Score=22.07 Aligned_cols=24 Identities=21% Similarity=0.412 Sum_probs=13.6
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+|.+|++-+..- .+..-+|+-||+
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~ 27 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGY 27 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCc
Confidence 566676654321 334567777766
No 44
>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=52.55 E-value=7.5 Score=18.63 Aligned_cols=8 Identities=50% Similarity=1.377 Sum_probs=5.4
Q ss_pred EEeeCCCC
Q 032192 111 FVCNFCGL 118 (145)
Q Consensus 111 w~C~lC~~ 118 (145)
|.|.+|+.
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 45
>PRK12860 transcriptional activator FlhC; Provisional
Probab=52.51 E-value=7.4 Score=30.45 Aligned_cols=31 Identities=35% Similarity=0.801 Sum_probs=22.3
Q ss_pred CCCeeeCCCCCc-eEcCceEEEeCCceEEeeCCCC
Q 032192 85 ESGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 85 ~~~~~RC~~C~a-YiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-.+.+|+.|++ ||-. ..+....++|++|.-
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 5522 224556799999997
No 46
>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=51.81 E-value=12 Score=27.45 Aligned_cols=31 Identities=26% Similarity=0.564 Sum_probs=21.8
Q ss_pred eeeCCCCCceEcCce-----------EEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFM-----------EFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~-----------~~~~~g~~w~C~lC~~ 118 (145)
..||..|.+-+-+-. .+......|+|+-||.
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 589999999553321 1233456899999998
No 47
>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=51.77 E-value=6.3 Score=25.85 Aligned_cols=31 Identities=23% Similarity=0.345 Sum_probs=15.9
Q ss_pred eeeCCCCCceEcCceEE----E-----eCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEF----V-----DNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~----~-----~~g~~w~C~lC~~ 118 (145)
-.-|++|++++=|-.+- . ...-.++|..||+
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 45799999988875332 2 2333588888874
No 48
>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=51.27 E-value=20 Score=20.19 Aligned_cols=25 Identities=20% Similarity=0.547 Sum_probs=15.8
Q ss_pred CCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
|..|+..| +.+-+..++. .|.-|+.
T Consensus 4 Cp~C~nlL--~p~~~~~~~~-~C~~C~Y 28 (35)
T PF02150_consen 4 CPECGNLL--YPKEDKEKRV-ACRTCGY 28 (35)
T ss_dssp ETTTTSBE--EEEEETTTTE-EESSSS-
T ss_pred CCCCCccc--eEcCCCccCc-CCCCCCC
Confidence 77788777 4444555544 6877775
No 49
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.90 E-value=6.5 Score=28.12 Aligned_cols=29 Identities=21% Similarity=0.258 Sum_probs=18.4
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~~ 119 (145)
....||..|+.+..+- ....+.|+-||..
T Consensus 69 p~~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPN-----ALDYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccC-----CccCCcCcCCCCC
Confidence 3468999999544221 1122459999983
No 50
>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=50.74 E-value=9.7 Score=21.23 Aligned_cols=14 Identities=21% Similarity=0.377 Sum_probs=10.2
Q ss_pred CCCeeeCCCCCceE
Q 032192 85 ESGLVRCCCCRGYR 98 (145)
Q Consensus 85 ~~~~~RC~~C~aYi 98 (145)
..+++||..|+.-|
T Consensus 14 ~~~~irC~~CG~RI 27 (32)
T PF03604_consen 14 PGDPIRCPECGHRI 27 (32)
T ss_dssp TSSTSSBSSSS-SE
T ss_pred CCCcEECCcCCCeE
Confidence 46789999998643
No 51
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=50.58 E-value=19 Score=23.55 Aligned_cols=28 Identities=25% Similarity=0.553 Sum_probs=22.2
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-++|..|+-- -+-|......-+|..||.
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 5899999854 355566777899999998
No 52
>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=49.58 E-value=13 Score=20.76 Aligned_cols=9 Identities=33% Similarity=0.851 Sum_probs=4.3
Q ss_pred eEEeeCCCC
Q 032192 110 SFVCNFCGL 118 (145)
Q Consensus 110 ~w~C~lC~~ 118 (145)
..+|.-|++
T Consensus 25 ~v~C~~C~~ 33 (38)
T TIGR02098 25 KVRCGKCGH 33 (38)
T ss_pred EEECCCCCC
Confidence 345555543
No 53
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=48.70 E-value=11 Score=22.56 Aligned_cols=32 Identities=22% Similarity=0.308 Sum_probs=22.8
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.+.++|..|+.-|...- .......|.|.-...
T Consensus 3 ~g~l~C~~CG~~m~~~~-~~~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRK-RKGKYRYYRCSNRRR 34 (58)
T ss_pred CCcEEcccCCcEeEEEE-CCCCceEEEcCCCcC
Confidence 46899999999987643 223446788887655
No 54
>PRK12722 transcriptional activator FlhC; Provisional
Probab=47.56 E-value=8.7 Score=30.00 Aligned_cols=30 Identities=37% Similarity=0.781 Sum_probs=21.6
Q ss_pred CCeeeCCCCCc-eEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~a-YiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-...+|+.|++ ||-.. .+....++|++|+-
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 45789999998 55222 24456799999998
No 55
>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=47.16 E-value=11 Score=20.78 Aligned_cols=26 Identities=31% Similarity=0.803 Sum_probs=12.7
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.+.|..|++=-+ | .+|..++|+-|++
T Consensus 2 ~p~Cp~C~se~~-y----~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 2 LPKCPLCGSEYT-Y----EDGELLVCPECGH 27 (30)
T ss_dssp S---TTT------E----E-SSSEEETTTTE
T ss_pred CCCCCCCCCcce-e----ccCCEEeCCcccc
Confidence 457888876332 1 4667799999975
No 56
>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=47.13 E-value=13 Score=21.86 Aligned_cols=22 Identities=32% Similarity=0.634 Sum_probs=15.8
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+.|..|+..| .|.+|+|..|..
T Consensus 1 v~Cd~C~~~i--------~G~ry~C~~C~d 22 (43)
T cd02340 1 VICDGCQGPI--------VGVRYKCLVCPD 22 (43)
T ss_pred CCCCCCCCcC--------cCCeEECCCCCC
Confidence 3688888733 355799999975
No 57
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=46.90 E-value=19 Score=29.77 Aligned_cols=29 Identities=17% Similarity=0.291 Sum_probs=21.5
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
---|++|++-|- -....+..+|.|+-|.+
T Consensus 245 GepC~~CGt~I~--k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 245 GEPCRRCGTPIE--KIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCCccCCEeE--EEEEcCCcCEeCCCCCC
Confidence 455999999983 33355667899999974
No 58
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=46.75 E-value=16 Score=27.94 Aligned_cols=10 Identities=40% Similarity=0.933 Sum_probs=6.2
Q ss_pred ceEEeeCCCC
Q 032192 109 KSFVCNFCGL 118 (145)
Q Consensus 109 ~~w~C~lC~~ 118 (145)
..++|++||+
T Consensus 148 ~P~~CPiCga 157 (166)
T COG1592 148 APEVCPICGA 157 (166)
T ss_pred CCCcCCCCCC
Confidence 3466666665
No 59
>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=46.73 E-value=8.5 Score=20.41 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=12.9
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+|..|++-|+-- .-+|+.||+
T Consensus 2 ~CP~C~~~V~~~--------~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPES--------AKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhh--------cCcCCCCCC
Confidence 477777776321 246777775
No 60
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.29 E-value=9.8 Score=27.46 Aligned_cols=31 Identities=19% Similarity=0.237 Sum_probs=18.8
Q ss_pred CeeeCCCCCceEcCc-eEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPF-MEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~-~~~~~~g~~w~C~lC~~ 118 (145)
...|| .|+.+...- ...+.-.-.|.|+-||.
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred eeEEe-eCcCcccccccchhccccCCcCcCCCC
Confidence 46899 999775432 11111111378999997
No 61
>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=45.47 E-value=12 Score=20.87 Aligned_cols=9 Identities=44% Similarity=1.287 Sum_probs=8.3
Q ss_pred eEEeeCCCC
Q 032192 110 SFVCNFCGL 118 (145)
Q Consensus 110 ~w~C~lC~~ 118 (145)
.|+|..||.
T Consensus 2 ~~~C~~CG~ 10 (34)
T cd00729 2 VWVCPVCGY 10 (34)
T ss_pred eEECCCCCC
Confidence 699999998
No 62
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.46 E-value=14 Score=27.01 Aligned_cols=32 Identities=19% Similarity=0.426 Sum_probs=19.7
Q ss_pred CeeeCCCCCceEcCce-------------EEEe--CCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFM-------------EFVD--NGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~-------------~~~~--~g~~w~C~lC~~ 118 (145)
...||..|+.....-- .+.. ....+.|+-||.
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs 115 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGS 115 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCC
Confidence 4689999996553320 0000 034588999998
No 63
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=45.08 E-value=6 Score=25.40 Aligned_cols=13 Identities=46% Similarity=1.002 Sum_probs=7.0
Q ss_pred CCCCeeeCCCCCc
Q 032192 84 GESGLVRCCCCRG 96 (145)
Q Consensus 84 ~~~~~~RC~~C~a 96 (145)
|+..|.||++||-
T Consensus 34 Ge~~I~Rc~~CRk 46 (61)
T COG2888 34 GEVEIYRCAKCRK 46 (61)
T ss_pred CceeeehhhhHHH
Confidence 3445556665554
No 64
>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=44.80 E-value=21 Score=18.66 Aligned_cols=23 Identities=30% Similarity=0.694 Sum_probs=14.2
Q ss_pred CCCCCceEcCceEEEeCCceEEeeCCC
Q 032192 91 CCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (145)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~lC~ 117 (145)
|.+|+.-|-|-- .+-.|.|+-||
T Consensus 1 C~sC~~~i~~r~----~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPRE----QAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcc----cCceEeCCCCC
Confidence 566766665542 24457888776
No 65
>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=44.65 E-value=6 Score=22.38 Aligned_cols=28 Identities=36% Similarity=0.727 Sum_probs=18.0
Q ss_pred CCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
|.+|++=-.|...-...|....||-|+.
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 7778887788877777777678998874
No 66
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=44.42 E-value=17 Score=26.80 Aligned_cols=24 Identities=29% Similarity=0.737 Sum_probs=19.0
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-|..|++=+ |..+|. -.|++|++
T Consensus 29 ~hCp~Cg~PL-----F~KdG~-v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPL-----FRKDGE-VFCPVCGY 52 (131)
T ss_pred hhCcccCCcc-----eeeCCe-EECCCCCc
Confidence 4699999876 446775 89999996
No 67
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=44.35 E-value=22 Score=28.94 Aligned_cols=28 Identities=21% Similarity=0.344 Sum_probs=19.9
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
--|.+|++-| -....-+..+|.|+-|..
T Consensus 245 ~pCprCG~~I--~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPI--RRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCee--EEEEECCCccEECcCCcC
Confidence 4588898877 333455677899998863
No 68
>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=43.78 E-value=7.5 Score=23.63 Aligned_cols=14 Identities=14% Similarity=0.494 Sum_probs=5.8
Q ss_pred EeCCceEEeeCCCC
Q 032192 105 VDNGKSFVCNFCGL 118 (145)
Q Consensus 105 ~~~g~~w~C~lC~~ 118 (145)
....+.|+|++|++
T Consensus 36 ~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 36 NQRTPKWKCPICNK 49 (50)
T ss_dssp HHHS---B-TTT--
T ss_pred hhccCCeECcCCcC
Confidence 34455699999985
No 69
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=43.67 E-value=30 Score=25.46 Aligned_cols=28 Identities=29% Similarity=0.682 Sum_probs=22.6
Q ss_pred eeeCCCCCceEcCceEEEeCCceE--EeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w--~C~lC~~ 118 (145)
=+-|+.|+. |=..+...++.| +|.-||.
T Consensus 97 yVlC~~C~s---PdT~l~k~~r~~~l~C~ACGa 126 (133)
T TIGR00311 97 YVICRECNR---PDTRIIKEGRVSLLKCEACGA 126 (133)
T ss_pred eEECCCCCC---CCcEEEEeCCeEEEecccCCC
Confidence 488999996 777777767776 8999998
No 70
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=43.12 E-value=18 Score=25.77 Aligned_cols=30 Identities=20% Similarity=0.234 Sum_probs=22.6
Q ss_pred eeCCCCCceEcCceEE----EeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEF----VDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~----~~~g~~w~C~lC~~ 118 (145)
.-|++|.++|=|..+. ..+.-.|+|-.||.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~ 90 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGT 90 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCc
Confidence 4599999988776544 33335799999998
No 71
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=42.82 E-value=7.6 Score=24.82 Aligned_cols=25 Identities=44% Similarity=0.984 Sum_probs=16.7
Q ss_pred CCCCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 84 GESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 84 ~~~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
|+..|.||.+||-.-|+ |+|+-||.
T Consensus 32 G~~~I~RC~~CRk~~~~----------Y~CP~CGF 56 (59)
T PRK14890 32 GEVIIYRCEKCRKQSNP----------YTCPKCGF 56 (59)
T ss_pred CCeeEeechhHHhcCCc----------eECCCCCC
Confidence 44558888888865543 56777764
No 72
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=41.82 E-value=41 Score=21.44 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=21.9
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-++|..|+.-- .-|......-.|..|++
T Consensus 11 ~VkCp~C~n~q---~vFsha~t~V~C~~Cg~ 38 (59)
T PRK00415 11 KVKCPDCGNEQ---VVFSHASTVVRCLVCGK 38 (59)
T ss_pred EEECCCCCCeE---EEEecCCcEEECcccCC
Confidence 48999999765 33455667799999999
No 73
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.77 E-value=16 Score=29.16 Aligned_cols=22 Identities=36% Similarity=0.937 Sum_probs=17.9
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-..|..|+. ..++.|.|.-||.
T Consensus 309 S~~C~~cg~---------~~~r~~~C~~cg~ 330 (364)
T COG0675 309 SKTCPCCGH---------LSGRLFKCPRCGF 330 (364)
T ss_pred cccccccCC---------ccceeEECCCCCC
Confidence 467998988 3366799999998
No 74
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=40.97 E-value=10 Score=22.35 Aligned_cols=10 Identities=30% Similarity=0.936 Sum_probs=8.1
Q ss_pred eeCCCCCceE
Q 032192 89 VRCCCCRGYR 98 (145)
Q Consensus 89 ~RC~~C~aYi 98 (145)
.||.+|++|=
T Consensus 2 ~kC~~CG~~G 11 (40)
T PF15288_consen 2 VKCKNCGAFG 11 (40)
T ss_pred cccccccccc
Confidence 5789999876
No 75
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.74 E-value=17 Score=27.33 Aligned_cols=27 Identities=30% Similarity=0.621 Sum_probs=19.3
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+--|.+|++-+. .-.+.-+|.||+|..
T Consensus 89 ~r~CARCGGrv~----lrsNKv~wvcnlc~k 115 (169)
T KOG3799|consen 89 TRFCARCGGRVS----LRSNKVMWVCNLCRK 115 (169)
T ss_pred hhHHHhcCCeee----eccCceEEeccCCcH
Confidence 455788888763 223556899999997
No 76
>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=40.49 E-value=10 Score=29.20 Aligned_cols=31 Identities=35% Similarity=0.670 Sum_probs=12.0
Q ss_pred CCCeeeCCCCCc-eEcCceEEEeCCceEEeeCCCC
Q 032192 85 ESGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 85 ~~~~~RC~~C~a-YiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-.+.+|.+|++ |+.-- .+....+.|++|.-
T Consensus 131 ~l~l~~C~~C~~~fv~~~---~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 131 MLQLAPCRRCGGHFVTHA---HDPRHSFVCPFCQP 162 (175)
T ss_dssp SEEEEE-TTT--EEEEES---S--SS----TT---
T ss_pred CccccCCCCCCCCeECcC---CCCCcCcCCCCCCC
Confidence 345799999997 44321 22355799999997
No 77
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=40.28 E-value=28 Score=28.21 Aligned_cols=27 Identities=19% Similarity=0.324 Sum_probs=19.4
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-|.+|++=|- ....-++.+|.|+-|..
T Consensus 247 pC~~Cg~~I~--~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIE--KIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCeeE--EEEECCCCcEECcCCCC
Confidence 3999998773 33345667899999974
No 78
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=40.27 E-value=16 Score=18.15 Aligned_cols=8 Identities=38% Similarity=1.265 Sum_probs=7.1
Q ss_pred EEeeCCCC
Q 032192 111 FVCNFCGL 118 (145)
Q Consensus 111 w~C~lC~~ 118 (145)
|.|.+|+.
T Consensus 1 ~~C~~C~~ 8 (25)
T PF12874_consen 1 FYCDICNK 8 (25)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 88999987
No 79
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=39.07 E-value=17 Score=25.71 Aligned_cols=9 Identities=33% Similarity=1.077 Sum_probs=8.5
Q ss_pred eEEeeCCCC
Q 032192 110 SFVCNFCGL 118 (145)
Q Consensus 110 ~w~C~lC~~ 118 (145)
.|+|-+||.
T Consensus 2 kWkC~iCg~ 10 (101)
T PF09943_consen 2 KWKCYICGK 10 (101)
T ss_pred ceEEEecCC
Confidence 699999998
No 80
>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=38.91 E-value=38 Score=18.29 Aligned_cols=25 Identities=24% Similarity=0.428 Sum_probs=12.3
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-|.+|++=+ .....+..-+|.-|+.
T Consensus 5 fC~~CG~~t----~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPT----KPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BE----EE-SSSS-EEESSSS-
T ss_pred ccCcCCccc----cCCCCcCEeECCCCcC
Confidence 367777654 3445667778887764
No 81
>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=38.82 E-value=17 Score=21.90 Aligned_cols=22 Identities=27% Similarity=0.611 Sum_probs=15.6
Q ss_pred eeCCCCCc-eEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRG-YRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~a-YiNp~~~~~~~g~~w~C~lC~~ 118 (145)
++|..|+. .| .|.+|+|..|..
T Consensus 1 i~C~~C~~~~i--------~g~R~~C~~C~d 23 (49)
T cd02338 1 VSCDGCGKSNF--------TGRRYKCLICYD 23 (49)
T ss_pred CCCCCCcCCCc--------EEeeEEeCCCCC
Confidence 47888884 33 156799999976
No 82
>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=38.26 E-value=29 Score=24.81 Aligned_cols=26 Identities=23% Similarity=0.612 Sum_probs=18.9
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
++.|.+|.+- |.. .+|..|+|+.|++
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 4678888863 232 3566799999999
No 83
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.85 E-value=31 Score=28.18 Aligned_cols=27 Identities=15% Similarity=0.229 Sum_probs=19.1
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-|.+|++-|- ....-+..+|.|+-|..
T Consensus 256 pC~~Cg~~I~--~~~~~gR~t~~CP~CQ~ 282 (282)
T PRK13945 256 PCRKCGTPIE--RIKLAGRSTHWCPNCQK 282 (282)
T ss_pred CCCcCCCeeE--EEEECCCccEECCCCcC
Confidence 5888888773 33345677899988863
No 84
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.28 E-value=33 Score=27.86 Aligned_cols=27 Identities=19% Similarity=0.317 Sum_probs=20.0
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-|.+|++-|- ....-+..+|.|+-|..
T Consensus 237 pC~~Cg~~I~--~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 237 PCPRCGTPIE--KIVVGGRGTHFCPQCQP 263 (269)
T ss_pred CCCcCCCeeE--EEEECCCCcEECCCCcC
Confidence 4999998773 33345677899999986
No 85
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=36.17 E-value=14 Score=35.18 Aligned_cols=35 Identities=20% Similarity=0.350 Sum_probs=28.1
Q ss_pred CCCCeeeCCCCCceEcCceEE------EeCCceEEeeCCCC
Q 032192 84 GESGLVRCCCCRGYRNPFMEF------VDNGKSFVCNFCGL 118 (145)
Q Consensus 84 ~~~~~~RC~~C~aYiNp~~~~------~~~g~~w~C~lC~~ 118 (145)
......||+-|.-.++.+... -.+.+.|+||+||.
T Consensus 349 ~~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~ 389 (958)
T KOG1074|consen 349 KPFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGN 389 (958)
T ss_pred cccccchhhhhHhhcCchhhhhhhhhccCCCCCeeeccccc
Confidence 346678999999999976654 34667899999998
No 86
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=36.11 E-value=21 Score=31.26 Aligned_cols=58 Identities=19% Similarity=0.267 Sum_probs=33.2
Q ss_pred hcCCceEEEEeecCCCCCCCCCC---ceecc--CCCCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 56 LSSMPSALMVQVLALPDPSEDPI---PVVDF--GESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 56 ~~~lPlg~~i~Pf~~~~~~~~~v---p~v~~--~~~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-.+|.-|-.|++.....++.-.| -++.. -...-++|.+|++=|..-= .+-|+|.-||+
T Consensus 313 a~~L~pGD~i~~~G~~~~~~~n~ek~~v~~l~~~~~~~p~Cp~Cg~~m~S~G-----~~g~rC~kCg~ 375 (421)
T COG1571 313 ARKLIPGDEITVYGSVKPGTLNLEKFQVLKLARYERVNPVCPRCGGRMKSAG-----RNGFRCKKCGT 375 (421)
T ss_pred HHhcCCCCEEEEecCccccceeEEEEEEEEeeeeEEcCCCCCccCCchhhcC-----CCCcccccccc
Confidence 35677777777765432221000 11100 1234579999999885432 11699999999
No 87
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=35.86 E-value=37 Score=24.17 Aligned_cols=27 Identities=33% Similarity=0.653 Sum_probs=21.0
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
=|.+|++.|-|-- +..+..+.|.-||.
T Consensus 4 FCp~Cgsll~p~~--~~~~~~l~C~kCgy 30 (113)
T COG1594 4 FCPKCGSLLYPKK--DDEGGKLVCRKCGY 30 (113)
T ss_pred ccCCccCeeEEeE--cCCCcEEECCCCCc
Confidence 4999999995543 44555899999998
No 88
>PRK10445 endonuclease VIII; Provisional
Probab=35.82 E-value=36 Score=27.51 Aligned_cols=27 Identities=19% Similarity=0.339 Sum_probs=17.0
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~ 117 (145)
-.|.+|++-| -....-+..+|.|+-|.
T Consensus 236 ~~Cp~Cg~~I--~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGII--EKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEe--EEEEECCCCcEECCCCc
Confidence 3477777776 33334566677777775
No 89
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=35.48 E-value=17 Score=25.95 Aligned_cols=27 Identities=22% Similarity=0.284 Sum_probs=17.5
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+.||-+|+....--..... --|+-||.
T Consensus 2 pH~CtrCG~vf~~g~~~il----~GCp~CG~ 28 (112)
T COG3364 2 PHQCTRCGEVFDDGSEEIL----SGCPKCGC 28 (112)
T ss_pred CceecccccccccccHHHH----ccCccccc
Confidence 6799999987644222222 24888887
No 90
>PRK00420 hypothetical protein; Validated
Probab=35.41 E-value=30 Score=24.79 Aligned_cols=25 Identities=32% Similarity=0.761 Sum_probs=18.2
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..|..|++ |+..+ .+| .-.|+.||.
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 56888984 55554 444 599999998
No 91
>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=35.10 E-value=36 Score=19.54 Aligned_cols=26 Identities=35% Similarity=0.920 Sum_probs=14.7
Q ss_pred CCCCCceEcCceEEEe--CCceEEeeCCCC
Q 032192 91 CCCCRGYRNPFMEFVD--NGKSFVCNFCGL 118 (145)
Q Consensus 91 C~~C~aYiNp~~~~~~--~g~~w~C~lC~~ 118 (145)
|..|++ ---|- |++ ....|.|+-|+.
T Consensus 6 CP~CGG-~DrFr-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 6 CPNCGG-SDRFR-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCC-ccccc-cccCCCCcCEEeCCCCC
Confidence 556655 11222 333 334699999975
No 92
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=34.11 E-value=41 Score=19.25 Aligned_cols=25 Identities=24% Similarity=0.418 Sum_probs=17.2
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNF 115 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~l 115 (145)
..|..|++.| .......|..|-|.-
T Consensus 2 ~~CP~Cg~~l--v~r~~k~g~F~~Cs~ 26 (39)
T PF01396_consen 2 EKCPKCGGPL--VLRRGKKGKFLGCSN 26 (39)
T ss_pred cCCCCCCcee--EEEECCCCCEEECCC
Confidence 3688899877 555555667777764
No 93
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=33.82 E-value=16 Score=25.52 Aligned_cols=28 Identities=21% Similarity=0.175 Sum_probs=18.3
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.|.||++|+=-.++ +.-...-+|+.|.+
T Consensus 57 ~Pa~CkkCGfef~~----~~ik~pSRCP~CKS 84 (97)
T COG3357 57 RPARCKKCGFEFRD----DKIKKPSRCPKCKS 84 (97)
T ss_pred cChhhcccCccccc----cccCCcccCCcchh
Confidence 48899999855543 22333567888876
No 94
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=33.68 E-value=30 Score=19.81 Aligned_cols=13 Identities=23% Similarity=0.498 Sum_probs=7.3
Q ss_pred CCeeeCCCCCceE
Q 032192 86 SGLVRCCCCRGYR 98 (145)
Q Consensus 86 ~~~~RC~~C~aYi 98 (145)
..+-+|.+|++..
T Consensus 17 ~~id~C~~C~G~W 29 (41)
T PF13453_consen 17 VEIDVCPSCGGIW 29 (41)
T ss_pred EEEEECCCCCeEE
Confidence 4455666666543
No 95
>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=32.83 E-value=44 Score=19.59 Aligned_cols=23 Identities=39% Similarity=0.944 Sum_probs=15.7
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~ 117 (145)
.|..|+ .|.++ +.+|+ -.|..|+
T Consensus 19 ~Cp~C~---~PL~~-~k~g~-~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCG---TPLMR-DKDGK-IYCVSCG 41 (41)
T ss_pred ccCCCC---CeeEE-ecCCC-EECCCCC
Confidence 577885 45665 45554 7899885
No 96
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=32.26 E-value=44 Score=27.96 Aligned_cols=41 Identities=22% Similarity=0.258 Sum_probs=26.5
Q ss_pred CceeccCCCCeeeCCCCCceEcCceEEEe---------------CCceEEeeCCCC
Q 032192 78 IPVVDFGESGLVRCCCCRGYRNPFMEFVD---------------NGKSFVCNFCGL 118 (145)
Q Consensus 78 vp~v~~~~~~~~RC~~C~aYiNp~~~~~~---------------~g~~w~C~lC~~ 118 (145)
+.+|.+.----+||..|+.||---..|+- ..-..+|..|+.
T Consensus 30 ~~~VRf~~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~ 85 (324)
T PF04502_consen 30 ILTVRFMMPFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSN 85 (324)
T ss_pred ceEEEEcCCccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCC
Confidence 44555432335899999999865555521 112468999998
No 97
>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=32.20 E-value=43 Score=27.20 Aligned_cols=26 Identities=19% Similarity=0.327 Sum_probs=18.0
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~ 117 (145)
-|.+|++-|- ....-+...|.|+-|.
T Consensus 247 pC~~Cg~~I~--~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 247 PCRRCGTPIE--KIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCeeE--EEEECCCCCEECCCCC
Confidence 5888888773 2334567788888884
No 98
>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=32.08 E-value=32 Score=17.69 Aligned_cols=12 Identities=33% Similarity=1.063 Sum_probs=8.5
Q ss_pred CCceEEeeCCCC
Q 032192 107 NGKSFVCNFCGL 118 (145)
Q Consensus 107 ~g~~w~C~lC~~ 118 (145)
+.+.+.|..|+.
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 345688888874
No 99
>PHA00626 hypothetical protein
Probab=32.03 E-value=51 Score=20.97 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=9.2
Q ss_pred CceEEeeCCCC
Q 032192 108 GKSFVCNFCGL 118 (145)
Q Consensus 108 g~~w~C~lC~~ 118 (145)
...|+|.-||.
T Consensus 21 snrYkCkdCGY 31 (59)
T PHA00626 21 SDDYVCCDCGY 31 (59)
T ss_pred CcceEcCCCCC
Confidence 45699999998
No 100
>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=31.34 E-value=35 Score=20.16 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=20.2
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..+..|..|+..|-. .....++|..|+.
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 458899999999922 3455799999997
No 101
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=31.31 E-value=26 Score=27.17 Aligned_cols=25 Identities=24% Similarity=0.546 Sum_probs=19.3
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-..||..|+-.+. ..+ =.|..||+
T Consensus 137 ~w~~rC~GC~~~f~------~~~--~~Cp~CG~ 161 (177)
T COG1439 137 KWRLRCHGCKRIFP------EPK--DFCPICGS 161 (177)
T ss_pred eeeEEEecCceecC------CCC--CcCCCCCC
Confidence 34689999998876 233 48999999
No 102
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.19 E-value=25 Score=32.43 Aligned_cols=24 Identities=25% Similarity=0.474 Sum_probs=18.6
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..+-+|..|+ |+ .|..|.|+.||.
T Consensus 624 ~~~~~C~~CG-~~--------~g~~~~CP~CG~ 647 (656)
T PRK08270 624 PTFSICPKHG-YL--------SGEHEFCPKCGE 647 (656)
T ss_pred CCCcccCCCC-Cc--------CCCCCCCcCCcC
Confidence 4578999999 44 355699999996
No 103
>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=30.12 E-value=30 Score=28.73 Aligned_cols=16 Identities=31% Similarity=0.841 Sum_probs=14.7
Q ss_pred EEEeCCceEEeeCCCC
Q 032192 103 EFVDNGKSFVCNFCGL 118 (145)
Q Consensus 103 ~~~~~g~~w~C~lC~~ 118 (145)
.|+.+|+.|+|+||..
T Consensus 135 vw~hGGrif~CsfC~~ 150 (314)
T PF06524_consen 135 VWDHGGRIFKCSFCDN 150 (314)
T ss_pred cccCCCeEEEeecCCC
Confidence 3799999999999998
No 104
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=29.99 E-value=21 Score=23.15 Aligned_cols=21 Identities=24% Similarity=0.474 Sum_probs=15.7
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..-|++|+.... .. +|+.||.
T Consensus 5 ~~AC~~C~~i~~--------~~--~Cp~Cgs 25 (64)
T PRK06393 5 YRACKKCKRLTP--------EK--TCPVHGD 25 (64)
T ss_pred hhhHhhCCcccC--------CC--cCCCCCC
Confidence 456999998772 22 8999998
No 105
>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=29.25 E-value=25 Score=21.25 Aligned_cols=10 Identities=30% Similarity=0.846 Sum_probs=8.0
Q ss_pred eCCceEEeeC
Q 032192 106 DNGKSFVCNF 115 (145)
Q Consensus 106 ~~g~~w~C~l 115 (145)
.+|+.|.|.-
T Consensus 10 ~DGK~WrC~~ 19 (46)
T PF08879_consen 10 NDGKGWRCSR 19 (46)
T ss_pred CCCCccccCC
Confidence 5788899975
No 106
>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=29.09 E-value=11 Score=23.39 Aligned_cols=29 Identities=34% Similarity=0.714 Sum_probs=23.1
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.|.+|++--.|...-...+..-.||-|+.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl 29 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGL 29 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHH
Confidence 38899998878777665566789999998
No 107
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=28.93 E-value=31 Score=19.33 Aligned_cols=14 Identities=36% Similarity=1.056 Sum_probs=11.4
Q ss_pred eEEeeCCCCCCccC
Q 032192 110 SFVCNFCGLDGRCL 123 (145)
Q Consensus 110 ~w~C~lC~~~~~~~ 123 (145)
.++|.+|+..|+.+
T Consensus 8 ~Y~C~~C~~~GH~i 21 (32)
T PF13696_consen 8 GYVCHRCGQKGHWI 21 (32)
T ss_pred CCEeecCCCCCccH
Confidence 48999999988754
No 108
>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=28.76 E-value=15 Score=26.02 Aligned_cols=27 Identities=30% Similarity=0.498 Sum_probs=17.7
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~~ 119 (145)
...||..|+.-..+-- ..+.|+.||+.
T Consensus 69 ~~~~C~~Cg~~~~~~~------~~~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDE------FDFSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHH------CCHH-SSSSSS
T ss_pred CcEECCCCCCEEecCC------CCCCCcCCcCC
Confidence 4689999998775432 23679999983
No 109
>PRK07218 replication factor A; Provisional
Probab=27.95 E-value=33 Score=30.03 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=18.9
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-+-||..|+=.+ ..|+|+.||.
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 4478999999887 2389999998
No 110
>PRK12496 hypothetical protein; Provisional
Probab=27.88 E-value=29 Score=26.22 Aligned_cols=25 Identities=24% Similarity=0.487 Sum_probs=16.5
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGLD 119 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~~ 119 (145)
-||..|+.+.+- +-..=.|..||+.
T Consensus 128 ~~C~gC~~~~~~------~~~~~~C~~CG~~ 152 (164)
T PRK12496 128 KVCKGCKKKYPE------DYPDDVCEICGSP 152 (164)
T ss_pred EECCCCCccccC------CCCCCcCCCCCCh
Confidence 689999976531 1111379999983
No 111
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=27.88 E-value=43 Score=24.34 Aligned_cols=28 Identities=18% Similarity=0.577 Sum_probs=18.6
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
++|--|+..- -..+....+.|.|.-|+.
T Consensus 1 v~C~fC~~~s--~~~~~~~~~~w~C~~C~q 28 (131)
T PF09779_consen 1 VNCWFCGQNS--KVPYDNRNSNWTCPHCEQ 28 (131)
T ss_pred CeeccCCCCC--CCCCCCCCCeeECCCCCC
Confidence 3677777654 233344455699999999
No 112
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=27.86 E-value=25 Score=18.28 Aligned_cols=22 Identities=27% Similarity=0.685 Sum_probs=12.9
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..|.+|++.+.+ + .-.|.-||+
T Consensus 3 ~~Cp~Cg~~~~~------~--~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP------D--AKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc------c--cccChhhCC
Confidence 468888884421 1 236777764
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=27.57 E-value=27 Score=30.93 Aligned_cols=30 Identities=17% Similarity=0.393 Sum_probs=15.1
Q ss_pred eeeCCCCCceE----------cCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYR----------NPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYi----------Np~~~~~~~g~~w~C~lC~~ 118 (145)
..+|.+|.+.+ ..||.+...- .|.|+-|+.
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 45566666544 2444443322 366666665
No 114
>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=27.46 E-value=42 Score=20.08 Aligned_cols=23 Identities=35% Similarity=0.803 Sum_probs=15.8
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
++|..|+..- . .|.+|+|..|.-
T Consensus 1 V~Cd~C~~~p--I-----~G~RykC~~C~d 23 (45)
T cd02344 1 VTCDGCQMFP--I-----NGPRFKCRNCDD 23 (45)
T ss_pred CCCCCCCCCC--C-----ccCeEECCCCCC
Confidence 3677787542 2 356799999986
No 115
>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=27.40 E-value=38 Score=24.53 Aligned_cols=31 Identities=23% Similarity=0.420 Sum_probs=21.8
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
...-+|..|+.-+-..... ...++.|..|+.
T Consensus 121 ~~~~~C~~C~~~~~r~~~~--~~~~~~C~~C~~ 151 (157)
T PF10263_consen 121 KYVYRCPSCGREYKRHRRS--KRKRYRCGRCGG 151 (157)
T ss_pred ceEEEcCCCCCEeeeeccc--chhhEECCCCCC
Confidence 4578888888777555554 445688888874
No 116
>PF12773 DZR: Double zinc ribbon
Probab=27.38 E-value=23 Score=20.82 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=17.7
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+-..|.+|++-+. ......++|.-|++
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcC
Confidence 4567777777775 33444577777777
No 117
>COG1773 Rubredoxin [Energy production and conversion]
Probab=27.38 E-value=35 Score=21.45 Aligned_cols=15 Identities=40% Similarity=0.884 Sum_probs=9.0
Q ss_pred EEeCCceEEeeCCCC
Q 032192 104 FVDNGKSFVCNFCGL 118 (145)
Q Consensus 104 ~~~~g~~w~C~lC~~ 118 (145)
|++--..|.|+.|+.
T Consensus 30 fedlPd~w~CP~Cg~ 44 (55)
T COG1773 30 FEDLPDDWVCPECGV 44 (55)
T ss_pred hhhCCCccCCCCCCC
Confidence 333334578888875
No 118
>PRK10220 hypothetical protein; Provisional
Probab=27.21 E-value=57 Score=23.43 Aligned_cols=26 Identities=19% Similarity=0.609 Sum_probs=18.7
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
++.|..|.+- |.. .++..|+|+.|++
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 4678888763 222 3566799999999
No 119
>PF14692 DUF4462: Domain of unknown function (DUF4462)
Probab=27.20 E-value=22 Score=19.38 Aligned_cols=13 Identities=23% Similarity=0.409 Sum_probs=10.5
Q ss_pred EeecccccCCHHH
Q 032192 41 RCSLNQIPCTENL 53 (145)
Q Consensus 41 R~T~~~iP~~~~~ 53 (145)
|++||.+|....+
T Consensus 5 r~~WN~LpRag~v 17 (28)
T PF14692_consen 5 RFNWNWLPRAGSV 17 (28)
T ss_pred ccccccCcccccc
Confidence 7899999987654
No 120
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.63 E-value=56 Score=20.49 Aligned_cols=24 Identities=42% Similarity=0.849 Sum_probs=18.8
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-.+..|.+|+.+.=| .-.|..||.
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGY 48 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCc
Confidence 347889999998855 368888887
No 121
>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 COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=26.05 E-value=39 Score=27.43 Aligned_cols=18 Identities=28% Similarity=0.508 Sum_probs=14.9
Q ss_pred CeeeCCCCCc-eEcCceEE
Q 032192 87 GLVRCCCCRG-YRNPFMEF 104 (145)
Q Consensus 87 ~~~RC~~C~a-YiNp~~~~ 104 (145)
.++||.+|++ .|+|-..|
T Consensus 145 ~~p~C~~Cg~~~lrP~VV~ 163 (250)
T COG0846 145 LIPRCPKCGGPVLRPDVVW 163 (250)
T ss_pred CCCcCccCCCccccCCEEE
Confidence 4789999999 88887766
No 123
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=25.92 E-value=32 Score=29.59 Aligned_cols=25 Identities=20% Similarity=0.336 Sum_probs=18.5
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
...-||.+|+== -..-.|-|+-|+.
T Consensus 352 ~~~YRC~~CGF~--------a~~l~W~CPsC~~ 376 (389)
T COG2956 352 KPRYRCQNCGFT--------AHTLYWHCPSCRA 376 (389)
T ss_pred cCCceecccCCc--------ceeeeeeCCCccc
Confidence 456899999832 2334699999998
No 124
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=25.52 E-value=31 Score=22.10 Aligned_cols=19 Identities=26% Similarity=0.693 Sum_probs=14.3
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-|++|+..+. .. +|+.||.
T Consensus 5 AC~~C~~i~~--------~~--~CP~Cgs 23 (61)
T PRK08351 5 ACRHCHYITT--------ED--RCPVCGS 23 (61)
T ss_pred hhhhCCcccC--------CC--cCCCCcC
Confidence 6899987772 22 6999998
No 125
>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=25.46 E-value=36 Score=19.53 Aligned_cols=12 Identities=33% Similarity=1.016 Sum_probs=7.0
Q ss_pred CCceEEeeCCCC
Q 032192 107 NGKSFVCNFCGL 118 (145)
Q Consensus 107 ~g~~w~C~lC~~ 118 (145)
.++.|+|+.||.
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 126
>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=25.41 E-value=40 Score=27.69 Aligned_cols=27 Identities=26% Similarity=0.630 Sum_probs=20.9
Q ss_pred eeCCCCCc---eEcCceEEEeCCceEEeeC
Q 032192 89 VRCCCCRG---YRNPFMEFVDNGKSFVCNF 115 (145)
Q Consensus 89 ~RC~~C~a---YiNp~~~~~~~g~~w~C~l 115 (145)
..|..|++ |+.-...-+.++++|.|+-
T Consensus 236 ~~C~~CGs~~s~LdEvi~dd~G~~~~~CSD 265 (277)
T PF06007_consen 236 GPCALCGSTDSFLDEVIDDDDGGRMFVCSD 265 (277)
T ss_pred CcccccCCCceeceeeEEcCCCCEEEEECC
Confidence 37888876 7777766678899999973
No 127
>PF14353 CpXC: CpXC protein
Probab=25.30 E-value=74 Score=22.47 Aligned_cols=9 Identities=56% Similarity=1.228 Sum_probs=5.0
Q ss_pred eEEeeCCCC
Q 032192 110 SFVCNFCGL 118 (145)
Q Consensus 110 ~w~C~lC~~ 118 (145)
.++|+-||+
T Consensus 38 ~~~CP~Cg~ 46 (128)
T PF14353_consen 38 SFTCPSCGH 46 (128)
T ss_pred EEECCCCCC
Confidence 455555555
No 128
>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=25.20 E-value=53 Score=20.37 Aligned_cols=23 Identities=39% Similarity=0.854 Sum_probs=17.3
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.+..|..|+.+.=|+ ..|..||.
T Consensus 25 ~l~~C~~cG~~~~~H---------~vc~~cG~ 47 (55)
T TIGR01031 25 TLVVCPNCGEFKLPH---------RVCPSCGY 47 (55)
T ss_pred cceECCCCCCcccCe---------eECCccCe
Confidence 478899999987443 57777776
No 129
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.01 E-value=39 Score=20.62 Aligned_cols=13 Identities=23% Similarity=0.409 Sum_probs=10.8
Q ss_pred CCeeeCCCCCceE
Q 032192 86 SGLVRCCCCRGYR 98 (145)
Q Consensus 86 ~~~~RC~~C~aYi 98 (145)
..++.|.+|+.+|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 5799999999764
No 130
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=24.18 E-value=30 Score=22.40 Aligned_cols=22 Identities=23% Similarity=0.694 Sum_probs=16.0
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
--|++|+..++. + .=+|+.||.
T Consensus 5 kAC~~Ck~l~~~------d--~e~CP~Cgs 26 (64)
T COG2093 5 KACKNCKRLTPE------D--TEICPVCGS 26 (64)
T ss_pred HHHhhccccCCC------C--CccCCCCCC
Confidence 358899887743 2 348999998
No 131
>PRK05580 primosome assembly protein PriA; Validated
Probab=23.89 E-value=33 Score=31.56 Aligned_cols=9 Identities=33% Similarity=0.737 Sum_probs=5.7
Q ss_pred eEEeeCCCC
Q 032192 110 SFVCNFCGL 118 (145)
Q Consensus 110 ~w~C~lC~~ 118 (145)
.|.|+-||.
T Consensus 421 ~~~Cp~Cg~ 429 (679)
T PRK05580 421 PKACPECGS 429 (679)
T ss_pred CCCCCCCcC
Confidence 366666665
No 132
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=23.37 E-value=61 Score=19.02 Aligned_cols=24 Identities=25% Similarity=0.491 Sum_probs=14.7
Q ss_pred eeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-..|..|+.. |. .|.+|+|..|..
T Consensus 4 ~~~C~~C~~~--~i-----~g~Ry~C~~C~d 27 (46)
T PF00569_consen 4 GYTCDGCGTD--PI-----IGVRYHCLVCPD 27 (46)
T ss_dssp SCE-SSS-SS--SE-----ESSEEEESSSSS
T ss_pred CeECcCCCCC--cC-----cCCeEECCCCCC
Confidence 4678888873 11 245799999864
No 133
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=22.94 E-value=56 Score=19.41 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=14.7
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+.|..|+.-. ..|.+|+|..|..
T Consensus 1 i~Cd~C~~~~-------i~G~RykC~~C~d 23 (45)
T cd02339 1 IICDTCRKQG-------IIGIRWKCAECPN 23 (45)
T ss_pred CCCCCCCCCC-------cccCeEECCCCCC
Confidence 3577777421 1356799999964
No 134
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.89 E-value=44 Score=31.29 Aligned_cols=24 Identities=29% Similarity=0.557 Sum_probs=18.1
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..+-+|..|+ |+.- -.|.|+.||.
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 6532 2399999996
No 135
>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=22.75 E-value=49 Score=15.87 Aligned_cols=8 Identities=38% Similarity=1.290 Sum_probs=6.5
Q ss_pred EEeeCCCC
Q 032192 111 FVCNFCGL 118 (145)
Q Consensus 111 w~C~lC~~ 118 (145)
|+|..|+.
T Consensus 1 y~C~~C~~ 8 (23)
T PF00096_consen 1 YKCPICGK 8 (23)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 68888886
No 136
>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=22.70 E-value=58 Score=19.47 Aligned_cols=23 Identities=17% Similarity=0.390 Sum_probs=15.1
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+.|..|+. .|. .|.+|+|..|.-
T Consensus 1 I~CDgCg~--~PI-----~G~RykC~~C~d 23 (43)
T cd02342 1 IQCDGCGV--LPI-----TGPRYKSKVKED 23 (43)
T ss_pred CCCCCCCC--Ccc-----cccceEeCCCCC
Confidence 45777773 233 356799998875
No 137
>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=22.70 E-value=56 Score=18.10 Aligned_cols=25 Identities=32% Similarity=0.505 Sum_probs=13.6
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
-...||.+|+.+.-| . .-.|+-|+.
T Consensus 9 l~~~rC~~Cg~~~~p------P--r~~Cp~C~s 33 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFP------P--RPVCPHCGS 33 (37)
T ss_dssp EEEEE-TTT--EEES----------SEETTTT-
T ss_pred EEEEEcCCCCCEecC------C--CcCCCCcCc
Confidence 347899999998622 1 257888865
No 138
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=22.68 E-value=38 Score=21.73 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=8.8
Q ss_pred CCeeeCCCCC
Q 032192 86 SGLVRCCCCR 95 (145)
Q Consensus 86 ~~~~RC~~C~ 95 (145)
.+.+||+.|+
T Consensus 35 ~D~irCReCG 44 (62)
T KOG3507|consen 35 GDVIRCRECG 44 (62)
T ss_pred CCcEehhhcc
Confidence 6799999997
No 139
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.67 E-value=40 Score=24.54 Aligned_cols=33 Identities=18% Similarity=0.402 Sum_probs=20.6
Q ss_pred CCeeeCCCCCceE-cCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYR-NPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYi-Np~~~~~~~g~~w~C~lC~~ 118 (145)
...+-|..|.++- --.-....+-.+|+|..|+.
T Consensus 28 ~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~ 61 (129)
T COG3677 28 ITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGS 61 (129)
T ss_pred cccCcCCCCCccceeeECCccccccccccCCcCc
Confidence 3446788888876 11111233356799999998
No 140
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=22.49 E-value=58 Score=23.50 Aligned_cols=26 Identities=19% Similarity=0.324 Sum_probs=18.9
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-.+|..|..++-+-. ..++|+.|+.
T Consensus 69 ~~~~C~~C~~~~~~e~------~~~~CP~C~s 94 (115)
T COG0375 69 AECWCLDCGQEVELEE------LDYRCPKCGS 94 (115)
T ss_pred cEEEeccCCCeecchh------heeECCCCCC
Confidence 4589999977774432 2356999998
No 141
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=22.49 E-value=66 Score=18.69 Aligned_cols=19 Identities=32% Similarity=0.917 Sum_probs=14.1
Q ss_pred eCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 90 RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
||..|...- ..|.|-.|+.
T Consensus 1 ~C~~C~~~~----------~l~~CL~C~~ 19 (50)
T smart00290 1 RCSVCGTIE----------NLWLCLTCGQ 19 (50)
T ss_pred CcccCCCcC----------CeEEecCCCC
Confidence 688887533 2599999987
No 142
>PHA02942 putative transposase; Provisional
Probab=22.43 E-value=56 Score=28.00 Aligned_cols=27 Identities=26% Similarity=0.427 Sum_probs=20.1
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.--.|..|+...- ...++.|.|.-||.
T Consensus 324 TSq~Cs~CG~~~~-----~l~~r~f~C~~CG~ 350 (383)
T PHA02942 324 SSVSCPKCGHKMV-----EIAHRYFHCPSCGY 350 (383)
T ss_pred CCccCCCCCCccC-----cCCCCEEECCCCCC
Confidence 3478999998542 22456899999999
No 143
>PF07627 PSCyt3: Protein of unknown function (DUF1588); InterPro: IPR013039 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=22.39 E-value=14 Score=25.90 Aligned_cols=23 Identities=26% Similarity=0.559 Sum_probs=16.7
Q ss_pred CeeeCCCCCceEcC----ceEEEeCCc
Q 032192 87 GLVRCCCCRGYRNP----FMEFVDNGK 109 (145)
Q Consensus 87 ~~~RC~~C~aYiNp----~~~~~~~g~ 109 (145)
.-.-|..|++.|+| |-.|+.-|+
T Consensus 68 ~~~~Ca~CH~~iDP~Gf~fE~fD~~G~ 94 (101)
T PF07627_consen 68 ENPACASCHRKIDPLGFAFENFDAIGR 94 (101)
T ss_pred CCCcHHHHhhhhCccchhhhccccccc
Confidence 45789999999998 445555554
No 144
>PRK04351 hypothetical protein; Provisional
Probab=22.24 E-value=99 Score=23.06 Aligned_cols=31 Identities=23% Similarity=0.246 Sum_probs=20.2
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.-.-||.+|+...--- --.+..++.|..|+.
T Consensus 110 ~y~Y~C~~Cg~~~~r~--Rr~n~~~yrCg~C~g 140 (149)
T PRK04351 110 NYLYECQSCGQQYLRK--RRINTKRYRCGKCRG 140 (149)
T ss_pred eEEEECCCCCCEeeee--eecCCCcEEeCCCCc
Confidence 3468898898754222 233446699999886
No 145
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=22.22 E-value=36 Score=21.93 Aligned_cols=13 Identities=31% Similarity=0.439 Sum_probs=10.7
Q ss_pred CeeeCCCCCceEc
Q 032192 87 GLVRCCCCRGYRN 99 (145)
Q Consensus 87 ~~~RC~~C~aYiN 99 (145)
-|+||-.|+..|.
T Consensus 3 iPvRCFTCGkvi~ 15 (62)
T PRK04016 3 IPVRCFTCGKVIA 15 (62)
T ss_pred CCeEecCCCCChH
Confidence 3789999998875
No 146
>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=22.22 E-value=27 Score=19.85 Aligned_cols=26 Identities=23% Similarity=0.361 Sum_probs=11.1
Q ss_pred CCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 91 C~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
|..|++..|-... ......+|-.||.
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 5555555554322 2222345555543
No 147
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.14 E-value=80 Score=22.07 Aligned_cols=31 Identities=23% Similarity=0.472 Sum_probs=22.6
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
.+..|.+|++. .--+.++.+...-.|..||.
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~ 50 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGL 50 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCC
Confidence 47889999963 33445556666789999998
No 148
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=21.74 E-value=1.1e+02 Score=23.79 Aligned_cols=28 Identities=29% Similarity=0.661 Sum_probs=21.7
Q ss_pred eeeCCCCCceEcCceEEEeCCceE--EeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~w--~C~lC~~ 118 (145)
=+.|..|+. |=..+...++.| +|.-||.
T Consensus 98 yV~C~~C~~---pdT~l~k~~~~~~l~C~aCGa 127 (201)
T PRK12336 98 YVICSECGL---PDTRLVKEDRVLMLRCDACGA 127 (201)
T ss_pred eEECCCCCC---CCcEEEEcCCeEEEEcccCCC
Confidence 589999996 666666655554 7999999
No 149
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=21.46 E-value=96 Score=23.38 Aligned_cols=31 Identities=32% Similarity=0.707 Sum_probs=18.4
Q ss_pred eeeCCCCCc------eEcCceEEEeCCc------eEEeeCCCC
Q 032192 88 LVRCCCCRG------YRNPFMEFVDNGK------SFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~a------YiNp~~~~~~~g~------~w~C~lC~~ 118 (145)
-+.|.+|+- |||.+-+.+..|. .|+|-+|++
T Consensus 30 kvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~r 72 (161)
T PF05907_consen 30 KVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKR 72 (161)
T ss_dssp EEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS-
T ss_pred EEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCC
Confidence 489999986 7888777765433 689999998
No 150
>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=21.20 E-value=90 Score=22.61 Aligned_cols=28 Identities=32% Similarity=0.765 Sum_probs=19.2
Q ss_pred eeeCCCCCceEcCceEEEeCCc--eEEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGK--SFVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~--~w~C~lC~~ 118 (145)
=+.|..|+ ||=..+...++ .-+|.-||.
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 38899999 55555544344 457999986
No 151
>smart00400 ZnF_CHCC zinc finger.
Probab=21.19 E-value=1.3e+02 Score=18.12 Aligned_cols=22 Identities=27% Similarity=0.563 Sum_probs=15.4
Q ss_pred cCceEEEeCCceEEeeCCCCCC
Q 032192 99 NPFMEFVDNGKSFVCNFCGLDG 120 (145)
Q Consensus 99 Np~~~~~~~g~~w~C~lC~~~~ 120 (145)
+|-..+......|.|--|+..|
T Consensus 12 ~pSf~v~~~kn~~~Cf~cg~gG 33 (55)
T smart00400 12 TPSFSVSPDKQFFHCFGCGAGG 33 (55)
T ss_pred CCCEEEECCCCEEEEeCCCCCC
Confidence 3445556666789999998744
No 152
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=21.12 E-value=54 Score=17.31 Aligned_cols=9 Identities=22% Similarity=0.837 Sum_probs=8.1
Q ss_pred eEEeeCCCC
Q 032192 110 SFVCNFCGL 118 (145)
Q Consensus 110 ~w~C~lC~~ 118 (145)
.|.|..|..
T Consensus 4 ~W~C~~C~~ 12 (30)
T PF00641_consen 4 DWKCPSCTF 12 (30)
T ss_dssp SEEETTTTE
T ss_pred CccCCCCcC
Confidence 599999987
No 153
>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=20.89 E-value=29 Score=29.90 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=23.0
Q ss_pred CCCCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 84 GESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 84 ~~~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
|.+-.--|.+|+.-++|--.... .|+|+ ||.
T Consensus 236 GKYh~~~c~~C~~~~~~~~~~~~---~~~Cp-CG~ 266 (374)
T TIGR00375 236 GKYHQTACEACGEPAVSEDAETA---CANCP-CGG 266 (374)
T ss_pred CccchhhhcccCCcCCchhhhhc---CCCCC-CCC
Confidence 45667899999988876543322 49999 999
No 154
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=20.83 E-value=63 Score=19.99 Aligned_cols=26 Identities=27% Similarity=0.543 Sum_probs=16.9
Q ss_pred eeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 89 ~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
..|.+|++=. |+- +. ..+|.|--||.
T Consensus 20 ~~CPrCG~gv--fmA-~H-~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPGV--FMA-DH-KDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCcc--hhh-hc-CceeEeccccc
Confidence 5699999422 332 22 23699999986
No 155
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=20.76 E-value=43 Score=22.16 Aligned_cols=13 Identities=31% Similarity=0.457 Sum_probs=10.9
Q ss_pred CeeeCCCCCceEc
Q 032192 87 GLVRCCCCRGYRN 99 (145)
Q Consensus 87 ~~~RC~~C~aYiN 99 (145)
-|+||-.|+..|.
T Consensus 3 iPVRCFTCGkvig 15 (71)
T PLN00032 3 IPVRCFTCGKVIG 15 (71)
T ss_pred CceeecCCCCCcH
Confidence 3799999999884
No 156
>PRK11827 hypothetical protein; Provisional
Probab=20.53 E-value=88 Score=19.93 Aligned_cols=28 Identities=18% Similarity=0.587 Sum_probs=21.2
Q ss_pred CeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 87 ~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
+++.|..|++=+- ++......+|..|+.
T Consensus 7 eILaCP~ckg~L~----~~~~~~~Lic~~~~l 34 (60)
T PRK11827 7 EIIACPVCNGKLW----YNQEKQELICKLDNL 34 (60)
T ss_pred hheECCCCCCcCe----EcCCCCeEECCccCe
Confidence 4889999999552 344556799999998
No 157
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.40 E-value=1.1e+02 Score=25.34 Aligned_cols=30 Identities=23% Similarity=0.568 Sum_probs=22.0
Q ss_pred CCeeeCCCCCceEcCceEEEeCCceEEeeCCCC
Q 032192 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGL 118 (145)
Q Consensus 86 ~~~~RC~~C~aYiNp~~~~~~~g~~w~C~lC~~ 118 (145)
....+|..|++ +... .+....-.+|.-||.
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 34678999997 3333 355666799999998
No 158
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=20.09 E-value=1.4e+02 Score=22.07 Aligned_cols=28 Identities=29% Similarity=0.742 Sum_probs=21.6
Q ss_pred eeeCCCCCceEcCceEEEeCCce--EEeeCCCC
Q 032192 88 LVRCCCCRGYRNPFMEFVDNGKS--FVCNFCGL 118 (145)
Q Consensus 88 ~~RC~~C~aYiNp~~~~~~~g~~--w~C~lC~~ 118 (145)
=+.|..|+. |=..+...++. -+|.-||.
T Consensus 102 yVlC~~C~s---pdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 102 YVICPECGS---PDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred cEECCCCCC---CCcEEEEcCCeEEEEcccCCC
Confidence 589999996 66666666664 57999997
Done!